While I enjoy theory crafting and I'm open to hear your further arguments I'm not seeing it myself. For one, according to Nasim our resident transmutation expert, it would take a powerful magic user a great deal of time and magical expenditure to permanently change someone's gender. It is unlikely that a peasant family could have anything to offer a magic user powerful enough enough to invest the effort. Not to mention something like that would surely go against Solansia's teachings and result in a fair amount of corruption in the target.
As for knowing that she is infertile because she is trans, if Alexia and Rowan were aware of that then why would they have been actively trying for the past 8 years? You'll need to point out the scene where Rowan says he knew before they got married that she was infertile as I don't remember coming across a scene like that. Personally, I've long held that is is just as likely that Rowan is the one that is infertile. In medieval times it was pretty common the lay the blame for conception problems at the woman's feet. ("Woe is me, I've had seven wives and each of them was barren, what are the odds.") However if we do assume that Rowan knew before hand I would imagine that something akin to medical diagnostic magic would be something much more accessible than permanent gender reassignment magic.
I would also argue that she clearly isn't used to having a penis as she during her futa scenes she marvels at it and expresses surprise as to what it is like.
As for the size differences in flash back scenes, I would first point out that as much as I love the art in this game the proportions of the character are not exactly super consistent. But assuming you are referring to this scene
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then Rowan is certainly taller. I can see how you would make the mistake however as the differing head to body ratios would imply that Rowan is shorter. But if you measure each character out Rowan is taller.
As for references to her previous gender I can't think of any, so if you can find a few of them I'd be interesting in having them pointed out.
I'm all for having a trans character (male or female) in the game, but I'm just not seeing it here. Maybe they will add someone in the next arc.