The game doesn't say that Amicus keeps constantly asking you to bottom, just that you had sex many times and he asked just a few times (and then stopped asking). And that the MC did not say he did not want to bottom, just that he's nervous about the size (he says "some other time," and there's nothing in the game to suggest he says that, because he can't say no to Amicus).
Adastra mirrors the sexual norms of our classical antiquity. Gay sex is frowned upon, but bottoming was seen as magnitudes worse than topping. Penetrating someone was about power and societal position. The handful of texts from that time that present gay couples positively religiously follow the rule that the older, more powerful, and more influential partner is the one doing the penetration.
So Amicus grew up in such an atmosphere. Being gay is bad and shameful enough, and he's also aware that he'd probably lose any claim to the throne, if he bottomed and that information got out to the public. So there's that, plus the fact that he just prefers topping, which is perfectly fine. He's also expecting you to say no. So he asks again, but he's mentally preparing to bottom (for the first time, btw). Even if you say yes he says "we don't need to do this at all," when he sees that you're nervous. So he's ready to do anything to be more intimate with you, since you'll be separated soon, but he puts your comfort first. Like during the first time, when he asks "is this okay," he's checking in with you throughout.
As to the second point, I agree with Esuriit. It's not like Amicus just wants to get off, he wants to be intimate with you (and no one else). I don't think there's anything wrong with him desiring you on a physical level.
The MC is a defined character and I got the feeling it was assumed that a) he's very much on board with the sex, and b) he'd prefer bottoming, but he's nervous, because of the size difference and the fact that he's never done anything before the timeline of the game other than some handjobs.
I don't know, after the fight before the second trial, I got the feeling that Amicus was nothing but considerate and respectful towards the MC.