Seems Legit
Taking a level of rogue (knife master and scout archetypes) and then a level of ranger (trapper and freebooter archetypes) is a legitimate combination. None of the archetype abilities replace other archetype abilities. Obviously, campaigns vary, so confirm the viability and availability with the DM, but this is mechanically sound.
There's Nothing Wrong With It...
But you're trading an extremely valuable class feature in your ranger spells for making traps instead. "But," you say, "I'm not casting spells until 4th level. I don't care." But you might. See, even though you can't cast spells and have no caster level at 1st level, you still have the ranger's spell list. This spell list lets you use magic items with the activation method Spell Trigger (Pathfinder Role-playing Game Core Rulebook 458), so while most 1st-level rangers can use a wand of cure light wounds, for example, you can't, and instead must rely on the Use Magic Device skill or some other method when wands are cheap and simple.
Further, while the game may never publish another trap usable by that archetype again, you can rest assured more ranger spells will be printed--it's a popular class whose origins date back to the hobby's beginning. And you'll never get access to those spells either despite being, at least nominally, a ranger.
Not having spells is huge in Pathfinder because if you're not using magic somehow you're toast, and usually the more you use the better off you are. At low levels, lacking magical access only stings--you won't have a lot of cash anyway and potions are the norm--but at mid- and higher levels when you could've used that wand of freedom of movement (a ranger spell!) to good effect and can't, it hurts a lot more.
Much of the same applies to the favored enemy class feature. Although the extraordinary ability freebooter's bane grants your party a +1 to attack and damage as a move action at 1st level, favored enemy is a +2 to attack and damage and other stuff all the time with no action cost at 1st level, albeit versus a limited class of foes. That last hurts a little, but unless the DM provides no campaign background, what you pick will come up (I mean, seriously, favored enemy (humans) is almost always solid), and that higher bonus is better--especially for a ranger who scouts and sometimes fights alone. Further, feats, magic items, and spells look for the favored enemy class feature on your character sheet, and probably nothing will ever look for freebooter's bane on your character sheet because favored enemy is what the historically popular ranger gets.
By giving up what the core ranger gets you cut yourself off from a lot of what the game expects you to have in exchange for what, in isolation, looks like a pretty good deal. When the character hits the table, though, the theory hits the fan, and you might be stuck really wanting to use that wand of cure light wounds, cast the spell hunter's howl, or wind a horn of antagonism instead of giving everyone a +1 to attack and damage or finding magical traps (which you could've just done as a rogue).
I'm really not trying to sell you on keeping the core class's class features--I seriously have no agenda here--, but the game expects you to have the core class's class features so it keeps churning out stuff that uses them, often to the exclusion of cool stuff found in splatbooks because those just aren't core, hence they appeal to fewer folks. Defying the game's expectations can be costly in the long run, and what's awesome at 1st level isn't always as awesome at 10th level. If you know the game's gonna crash and burn by session 3, this seriously won't matter much (although being able to confidently wield a wand of cure light wounds is awesome all the time), and you can do whatever. But for a long-term campaign, consider carefully before rejecting the core.
That is a lot of questions, actually.
Fly
PFSRD on the matter:
You generally need only make a Fly check when you are attempting a complex maneuver. Without making a check, a flying creature can remain flying at the end of its turn so long as it moves a distance greater than half its speed.
The complex maneuver table there lists the actions possible (fly slowly, hover, turn sharply, ascend steeply). Less drastic maneuvers should be generally possible without a check. Please also note, that it gets a modifier to the Fly check from its maneuverability and size.
The Wingover feat allows it to turn 180 degrees for free once per turn, as opposed to expending movement and making a Fly check.
Attack
Talons are claws on the bird's feet. They are accessible when it is airborne; they are even accessible when it is standing on the ground (jumping a bit with a bit of help from wings).
It can attack 3 times if it takes a Full attack action; it is possible maintain an airborne position in that case with a successful Fly check to hover (since Fly checks do not consume an action). Please note that this method is not dependant on Wingover feat.
Without the Multiattack it does get a -5 modifier to all secondary attacks.
Which attack is primary or secondary depends on the attack type, and is indicated in the Universal Monster Rules for Natural Attacks. Bite, claw, gore, slam, sting and talon attacks are always primary. Other attacks can be primary if a creature doesn't have any of the aforementioned types. Primary attacks use the full Str modifier to damage (or 1.5x if the creature only has a single natural attack, or for special cases), secondary attacks get only 0.5x Str to damage, and are made at a -5 modifier (or -2 with the Multiattack feat).
For the Roc, all listed attacks are primary and get full Str to damage. The Multiattack feat has no effect since it only affects secondary attacks.
Tricks
Simple movement does not trigger a Fly check; a steep ascend and a sharp turn, on the other hand, does.
The attack of opportunity is triggered by many things, but in relation to movement it is triggered when someone leaves a threatened square. So if it initially was not in anyone's reach, an optimal movement to flanking position probably won't trigger any AoO's, since it will only enter a threatened space.
Maintaining a flanking position, given the opponent does not move, is a matter of a Fly check to hover (or standing on the ground), so no AoO's here.
Best Answer
It would be a free action for the Skirmisher's companion to activate the trick when it hits, after the Skirmisher took a free action to command the companion to attack something. As per the Skirmisher Tricks
None of this modifies how the trick is activated, apart from shifting the activation to the companion.
The default for commanding an Animal Companion is a Free Action for a normal Hunter, Ranger or Druid, thanks to Link.
According to the description, the Animal Companion makes the decision on when to use the trick, although since the companion is obeying the commands of the Skirmisher, and since the Skirmisher player is generally controlling the animal companion, this would mean the player is choosing when to apply the trick. For an in-universe explanation of this mechanic, I take it to mean that when the Skirmisher directs his Animal Companion to attack, he includes a command to apply Hobble, if able, rather than the animal deciding when to use it. e.g. "Go for the legs, Boo!"