The Rules Don't Say
As nvoigt pointed out, the PHB describes chain mail and plate mail as complete items. They are either on, or they're off. There are rules for how long it takes to put them on and take them off, but there is no description for your AC while wearing just the padding.
Furthermore, the padding under plate and chainmail isn't padded armor. Padded armor is a different thing. When you buy plate mail you don't get plate mail armor that has padded armor inside, you get plate mail armor that has padding inside.
You Could Try It
Since there are no rules that describe this situation, you are down to the most general rule of all. At the beginning of the Players Handbook, it says:
1.The DM describes the environment. ... 2.The players describe what they want to do. ... 3.The DM narrates the results of the adventurers' actions. (PHB p.6, "How to Play")
So, your character could just try it and see what happens. "Try it" could mean a lot of things. "My character takes off all his armor but the padding. What's his AC?". "I'm looking at the swamp we're about to cross. I'm an experienced fighter, I've been wearing armor for years, I've been trained by experts. I know if I fall in wearing full plate, I'll probably drown before I can get out of it. What does my training tell me about whether I can wear just the padding in order to mitigate the drowning risk but still retain some protection?" Or perhaps your armor wearer might consult armor experts.
You've Solved My Drowning-in-Armor Puzzle!
As a GM, I view the water-armor situation as a challenge or problem for the PCs. Which do you do, take off the armor and carry it thereby lowering your AC, or wear it and risk drowning?
Only it isn't an either-or, which is the beauty of RPGs. There are other solutions to the problem. Perhaps the water is such and the PC's strength is such that the PC can just walk out, perhaps with a strength or constitution check. Perhaps the PCs have access to magic that allows them to breathe water. Maybe they can bypass the swamp. The players might (and hopefully will!) have innovative solutions I haven't thought of.
If the PC said, "I take off most of my armor, and wear only the padding", or "only the helmet, gauntlets, greaves and leg guards" and subsequently fell into the water I think the time to remove the armor and thus the risk of drowning would be less, while the chances of swimming in part of the armor would be more. And if the PC were attacked by Rodents of Unusual Size while crossing the swamp, I'd definitely have to allow that the PC's base AC in padding or other bits and pieces was greater than without armor. Wearing only part of the armor might be a reasonable solution to the but-I-might-drown problem. Although wearing only the padding might be really bad for it, given briars and such.
Given that I don't want to play "Armor & Anoxia" I'd be reluctant to come up with a codified houserule that says you can wear half the armor for half the AC and half the risk of drowning, but perhaps that would be the solution. I'd definitely want to keep things liquid, and not weigh the game down with heavy armor questions, but I'd definitely want to pad it enough to keep things moving forward, while at the same time rewarding innovative role-play and problem-solving.
No. A few things to note that stand out
crafting bonuses at lv. 3. Being able to gain the equivalent of a current lv 10 ability for artificers at lv 3, even if only for one kind of object is overpowered. Being able to gain powerful armor so early in the game seems cool, and is, but it is way too powerful at such a low level.
too flexible. With all these available options at lv 5 and increasing, this gains too much flexibility for a subclass. Consider that one of the main properties of the warlock is the eldritch invocation, and that you have a similar amount of special abilities as invocations for the entire class, as one of the class's main features, and you can see that for a sublcass, this is way too good.
Lackluster higher abilities. I get that heavily armored is supposed to be it's main thing, and it's scaling is most of the subclass, but the higher abilities are so underwhelming that they almost might as well not exist. The sixth level thing is confusing, and better suited as part of the original ability, and martial weapon proficiency at lv 14? I don't want to harp too much, but that is way too late to be gaining proficiencies in weapon types. At that point your character should know what weapons they want to be using, not gaining proficiencies in all martial weapons.
Inbalances in the main feature. The main feature, as mentioned previously, is obviously the Heavily Armored ability. At level 17 you can use the majority of your subclass' ability into casting a cantrip as a bonus action, while at the same time at lv 12 you have protection from most mind manipulation, and at just lv 8 you can essentially be the ultimate underwater explorer. These are quite large differences, and the problem is that in the quest for diversity in options while retaining balance, most of these abilities come across as bland, and not particularly diverse at all.
Confusion with the main ability. The AP points don't make much sense to me. You start out by saying you spend them to enchant the armor, but then all the later abilities require using them (and not a small amount of them), but only at later points in time. You need to clarify if you need to save points, or if you can unenchant things later or what. Also, either way, the limit on how many you have versus how many you spend on later abilities makes them quite limited, when you generally just want to have cool enchanted armor
It's not all bad. I do like where you are going with this though, regardless of what I have just pointed out, and I don't want to feel like all I'm doing is shutting you down here. I'm not. I really like the idea. I really like the basis behind the main ability. I love the idea of an armor-enchanter. It just still needs work
All and all, I really like where these ideas are coming from, but it needs a lot of work. By trying to create diversity while retaining balance you seem to have achieved neither. So here's my advice.
Move the armor creation ability back. It's just too powerful for a lv 3 character to have
Move up martial weapon proficiency. At lv 14, people either have martial weapon proficiency, or they don't. And if they don't they've already built around that, so essentially the proficiency at this point is pointless.
Consolidate the armor enchantments. Instead of having so many different enchantments that don't get any job done that they are supposed to, make a few packages that get better as you level up. Like this:
Mind Protector (Requires 10 AP): You gain immunity against mind controlling effects created by spells of level 3 or lower. For every extra 2 AP spent on this enchantment, the spell level it protects against increases by 1.
Have a few sets like this, and you can have diversity, utility, and balance all in one, without being too much or too little of any.
Change the other AP abilities. The other AP abilities are just confusing with how AP works. Instead make them into enchantment sets of their own, or build them into every set, as I describe next
After this, you might need some more abilities. Not to worry. A good way to do this could be to have the abilities of each enchantment set get an enhancement. Perhaps have an ability added to each, that lets you de-level them in exchange for a temporary boost. Something like that. Or, create new abilities that just give all of your enchanted armor some bonuses. That would work as well
I really hope that all of this helps you. I can't wait to see how you change this for it's next version, and I hope that this helps gives you a feel for what needs changing in that next version.
Best Answer
The intent is obvious: you cannot wear Arcane Armor and another suit of armor.
The rules for “Multiple Items of the Same Kind” state:
The rules for Arcane Armor are written with this in mind - you can only wear one suit of armor. So it is entirely natural that the rules would not address what happens if you are already wearing two sets of armor when you convert one to Arcane Armor: you aren’t supposed to be wearing two, so there’s no need to explain what happens when you are. So if we have an unusual exception to the general rules, like you happen to be wearing two armors at once somehow, we shouldn’t be surprised when strange things happen or the rules become muddy.
So yeah, if you want to be pedantic in your rulings, you can use this as a work around as the strictly technical reading allows you to do this, but the intent is abundantly obvious: it doesn’t work that way. To be clear, there is nothing inherently wrong with being pedantic in your rulings, I’m quite proud of my most downvoted answer. Just make sure you talk about it with the table if you are going to insist on using a ruling that is quite obviously against the intent of a feature. And if you are not the DM, don’t get upset when they rule that your idea doesn’t work.