Mmmm yes I know what you mean. I am not sure I would have written it myself as it creates so many problems, but this is Jim's party, as they say. Hopefully Jim does a really good Time Travel book - it seems he has already begun to lay the foundations in Cold Days so I expect Mirror Mirror to be very enlightening (and will be rather disappointed if it is not). But notoriously difficult and tricky to write too, considering the physics isn't even that clear on how it should all work (and there are many theories, and interpretations of those theories)! But you are tying my head in a pretzel with your questions about multiple Harry's. I suppose you question assumes that all possible Harry's exist, rather than just some. If it is just some, then they would likely tend towards being the same (consider the Law for the Conservation of History, as Harry puts it). But if they all exist then likely there is at least one Harry that doesn't ever act against his nature, probably because the Devil has won in that creation (if not several versions). Which I imagine means Uriel or one of the other Archangel's nuke the whole thing at that point. I see the whole war being like an enormous game of Go or Mahjong...it's not about winning one game, but the set. But it is rather a bleak view of existence. But to answer your question, no. Harry always has Free Will -whether he chooses to use it or not is an entirely different matter. Just because he never has exercised his ability to Choose, doesn't mean he can't. Your conclusion is wrong because one of the premises of your argument is false - Free Will is NOT the ability to choose to act against one's nature. Free Will is the ability to Choose. Period. It only matters whether you can Choose, not whether you act in accordance with your nature, or against it. Quite probably what the Devil is so upset about, at least in the Dresden Files.
The whole timeline thing has the same problem as the Base-Reality theory (which is popular amongst the computer simulation crowd - a la the Matrix - which of course is just a much older theory with a new coat of paint). Which is the first Time Line? How could you even tell? Is it more important than all the others? Does it still exist or did it fail? That is too deep a rabbit hole for this discussion I suspect, fun as it is.
As for the Antichrist issue - well, that is an interesting way of looking at it. Drakul fits the role with what he is, rather than it being integral to his origins. Like if a person is a fireman. You are not necessarily born one, but you can become one by your choices and your actions.
But. To answer your question about why the Devil can't have several - just reading it gave me the answer. Because I suspect it is against his very nature. Commonly, TWG is equated to be similar in most aspects to the Christian God. The God of Love. Harry says the act of creating a child, a soul, is a fundamental act of love. Two souls combining to create a new third soul, separate from the original two. Now you could argue that definitely love is often not involved in creating a child, and Jim often leaves things very vague and mystical in this area, but you could imagine at the point that TWG creates that new soul, that is an act of Love. I really have no idea how Jim looks at this in his world, and I suspect we will never ever get a clear answer as it probably runs too close to his own views (and Jim is quite private about that stuff).
So I think unless the Devil fell in love, he couldn't make a soul. It requires a full-on act of love. And the Devil cut himself off from Love, or so we are led to believe (unless he actually serves a purpose in Creation). Maybe that's how it happens and then he gets mad when something goes wrong. Who knows? Unlike Dresden though, he really could burn the entire world.
The other side of this is of course, that in creating an Antichrist or several, he is really just creating the possibility of an Antichrist. And that because his child would be half-mortal, they get the freedom to Choose. Which I imagine would piss him right off.
JUST TO BE CLEAR TO ANYONE READING - this is purely a discussion for how things might work in the Dresden Files. It doesn't necessarily reflect my views, and isn't gospel in our world. So please don't get mad. I know this is skirting a tad close to Touchy Topics so I am doing my best to stay away from the line.