To make your question short, and to see if I understood it correctly, we're talking about a player who made his character a certain one and roleplays it entirely different. You added that you think that it comes from inexperience, and that he created this character after you said "no" to some "freak-character"-ideas. You want to help him roleplay the character he created.
As I see it, this problem is made from two smaller ones. The first is that he doesn't see his character as interesting because the character "is normal and normal is boring". The second is that you wanna help him understand why the way he plays the character does not fit the story-world of your game.
Helping him understand that "normal is not boring
This is the more important problem, as it stands in the basis of the entire problem. If he'll see that normal characters can be interesting his "anti-persona" will perish and he'll roleplay a normal character and not a freak one. The main trick here is to show him that normal characters are not entirely normal, i.e. "no person is like the others". In order for that to work, we need to give the character depth.
The easiest way to give depth to a character is through internal conflicts. Having goals and all is nice, but without something that blocks oneself from achieving them it is far less interesting. First thing to do is to go over his character's background and see if he implemented there an internal conflict for his character. If so, show it to him and talk with him about it. If no, sit with him and help him to come with one. The internal conflict doesn't have to be extravagant, but it needs to be there. An example one might be that he loves Vincent's sister but secretly hates Vincent himself, or another like Loves the sister but thinks that he's not good enough for there. I'll take the second one as an example for this section.
The conflict gives us a few things, a few added benefits. It gives the character 2 conflicting goals: "Get the sister and prove that I'm worthy". Now, with those two we also get a kind of an achieving-plan: "If I'll show her that I'm worthy, by getting something amazing done, she'll want me and I'll be able to get her". More than that, the character gets the knowledge that each advancement in order to achieve one goal will drive the other one to the far end.
But the first conflict is even more interesting. The character here has the knowledge that he needs the brother in order to save his lover, but he just can't stand being near the brother. He'll drive the mission onward for two reasons but he'll have doubts about his lover- if he'll marry her he'll be stuck with this brother of hers.
To make long story short, simple conflicts can show the player that even normal characters are interesting and unique. When combined with goals they force the character to take certain steps along the roads, to commit certain actions along the way, that he won't want to do but will make him doubt himself and question himself and see that his problem are far more interesting than those of every freak that he'll encounter.
Another nice way to help him see the importance of conflict is through showing him and analyzing with him certain protagonists that are normal people, from the stories and movies and series (of any form)that he likes. He'll see quite quickly that the conflicts make them interesting.
But he may say that it is not enough. For that there are a few more literary tools that might help him see why normal people are interesting. The first one is having flaws (internal or external) and the second one is using "The Ghost".
Flawed characters are characters that just like normal people aren't perfect. Those flaws can be internal (self-doubts, for example, or a mild paranoia) or they can be external (they're look frightens ordinary people, for once, or a missing hand for the other). The idea is that the character has to deal with the flaw, and one day to find the strength to overcome it. The fight for the overcoming act makes the character far more interesting. A nice example of that can be seen in The Rain Man, where he learns at the end that he can count on strangers/"dumb" persons like he's brother. Another nice example can be seen in the story of The Ugly Duckling who although looking terrible learned to acknowledge himself and to accept the way he looks, to accept his difference.
"The Ghost" is an event from the past that just like a ghost haunts the character to this day. Again, trying to cope with it is what builds a deep character. One example for this can be seen in the movie Inception, where we literally have a ghost- Cob's wife. Another example for this can be seen in the movie Casablanca, where he has to deal with his broken relationship with Ilsa. This Ghost is far more interesting as the originator of the Ghost actually comes back to his life. In Frozen we see another kind of a Ghost- the act that one feels guilty about. Elsa actually killed her sister.
All of these techniques are there for one reason- to make regular people interesting, to give depth to the characters, to make them human beings with goals and drives and psychology.
Helping him see that his character doesn't fit the world
After he understands that he doesn't have to be a freak in order to be interesting, he will be far more understandable about playing a character that fits the world. Then, try to explain to him as calmly as you can what it is in the way he played his character that doesn’t fit the world.
Explain to him that the characters are in a world where being a freak is bad, where achieving one's goals is the ideal. Each and every one for himself, as the saying goes. Give him examples from the way he played his character and analyze with him, in a one-on-one conversation where his way of acting came from. Use the background he created to illustrate to him where your problem comes from.
Then ask him what problems he has with his character, and together try to find a solution. Maybe let him be just a little bit freakish. Maybe he needs to just create a different character. This is basically between you and him. After that show the updated character to the group and get their approval.
When combining those two, you'll get a player who his far more willing to both play the character while also seeing the problems with the way he played his character before.
Combining the two solutions
When combining the two solutions you get a better player, who understands for the future also how to create regular characters that are not freaks yet far more interesting than those freaks will ever be able to be. Furthermore, you get a player who is willing to play his character as written while still making the character fit into the world. Hope any of these helped you.
Your first question is about half a GM problem, and half a player/PC problem. I've been on both sides of this issue: GMing for a character who had little reason to participate in the story with the other PCs, and playing a character who had no reason to participate in the story and every reason to run wildly in the other direction. In both situations, the solution has two parts:
The GM finds ways to include the PC in the plot.
It sounds like your group is already doing this, but for posterity: this means that the GM must look for ways to actively involve the PC in the story, by using their background hooks, talking to the player about what the character might find interesting, and otherwise looking for ways to help the character find motivation within the story to participate in the story.
You do need to be careful not to change the story or the game's focus so much that the other players begin to feel excluded or ignored, but this is a matter of understanding your group, finding a balance, and getting buy-in from the player of the problem PC. Which brings me to part 2 of the solution:
The player finds ways to include their character in the plot.
This is the much harder part of the solution: the player must meet the GM halfway, otherwise the game becomes "The Problem PC Show!" and no one else has fun. This may mean the player has to bend or tweak the character in some way - not enough to compromise the core of the character, but enough to keep them with the group when otherwise they wouldn't stay.
This is, admittedly, difficult to do. Some people are so attached to their characters that they're unwilling to compromise; or they simply can't see a way to bend the character on an issue without breaking them completely. However, it's absolutely required in order to solve this problem.
Why player buy-in makes a difference:
When I played a character who had no reason to participate in the story, I looked hard for ways to make her want to be there. But all logic dictated that she run far away, find a hole, and pull it in after herself, so any other choices felt wrong to me. This showed in my roleplaying, and ultimately caused much frustration for our whole group as session after session became centered around getting her involved when she didn't "want" to be.
I put "want" in quotes there for a reason. Players with especially strong "my guy" syndrome (which I know I'm prone to) will insist that they're "just playing their character" and that "the character can't be changed". But when I GMed for a character who had no reason to be there, his player was willing to meet me halfway, and the result was a fun campaign for everyone where that character even made a large part of the highlight reel.
The reason it worked was because the player was willing to say, "he has no reason to come along, but does anyway, because that's how group-based RPGs work." We hand-waved it a bit as "he has nowhere else to go and nothing better to do", but really that character should have been as long-gone as mine wanted to be. But because the player was willing to take the meta option and bend his character enough to say "screw it, he's participating" without looking for a story reason, it worked. It kept the game from focusing too much on that character, but meant he was still there when story developments happened that he was interested in, thus giving him the time he needed to organically grow interested in the plot.
When the player isn't interested in the scenario
This part is a little trickier. If the player doesn't buy Dresden's world, including all the magic elements, what's he doing playing a Dresden Files game anyway? You and your co-GM need to talk to this guy privately, out of game, and ask him why he's playing. If he just wants to hang out with your group and doesn't care much about the game, then you need to address that. Maybe give him a character with a minor support role, so that he doesn't need to participate much in the game and can just hang out; maybe say that if he just wants to hang out, the game isn't the time for it and you'll find other group activities he can participate in. It's up to you and your group to decide what's best here.
If he insists that he wants to play the game, then you need to find out why he's actively sabotaging it. Tell him that his actions suggest he doesn't want to play, and in fact are making it harder to play. It's possible you simply have an attention hog on your hands, in which case you should deal with him appropriately. (I'd suggest going through the problem-players tag, as there are a number of questions and answers you may find relevant depending on your exact situation.)
TL;DR: The GM and the player need to meet halfway on adapting the character and the world. But if the player isn't buying the game's scenario in the first place, then that must be addressed first.
Best Answer
Here are a few methods that have proven to work for me:
You provide the long-term motivation for his character background to him. Classic is a missing and beloved person, that they are searching for (sister, father, etc.) and traveling around the world to learn something about while funding themselves with adventuring. Or it could be a big goal like owning a barony or something. Or the character has unsettling dreams that beckon him to go somewhere or do something. If they have difficulty to come up with such stuff, and you don't, and they don't mind, you can just help them with it.
Their character has no long term motivation, but from the initial adventures develops friendships and relationships with the rest of the party. As he has nothing better to do, and his friends can use his help, he decides to come along on whatever it is they are up to. The upside of this option is that it is entirely independent of campaign story arcs.
Their character has no intial long term motivation, but as part of the inital adventures gets drawn into a larger plot, and to save and protect those he cares about, has to pursue it. This can be anything from a looming invasion wiping out his country to an evil archcleric trying to end the world. If your campaign has a larger plot and is not just a sandbox of random adventures, you likely already know what this would be.
P.S.
If this is even a problem depends on how you want to play. There are enough tables, where the deeper motivation of the PCs is not important, as long as there are monsters to slay, treasures to loot, and XP to collect. From you asking the question, it seems it is a problem for your table, or at least for you. If it is mostly you yourself who feels the need to have motivation for his character, but neither he nor the other players fret about it, then you could just let go of that, and move on.