There is probably some deep philosophical discussion to be had here on what defines a man or woman. There's a contingent of people who feel like they are in the wrong bodies in the real world right now. I can't really speak to any of that, but I don't know that it's a major factor when it comes to fiction anyway. While transformation stories aren't something I seek out, it doesn't really bother me that much, so I'll try to dig into my thoughts on it personally.
I think there's some overlap with people who can enjoy a female protagonist game. There's a degree to which you already put yourself in the shoes of the female character when you play a game like that. Having a transformation element in the game just makes it part of the story. I think the basic concept is what if a woman had the sex drive of a man. Some might argue there are already women with stronger sex drives than some men, but that's beside the point. The basic math is men = horny, women = sexy; man brain -> woman body = horny and sexy. Often the transformed character is put into situations against their will. This follows most female corruption games where things are done to the character, at least at first. There are some fish out of water and new experiences aspects to it as well.
I think at this point it helps to be able to separate clearly in your mind having a fictional character do things and doing them yourself. I don't think having a female character choosing to fuck a man in a game is gay. I don't think it's gay even if that female started as male. At that point in the game, the character is a woman to me and the character is also not myself. The end result is still a man and woman having sex regardless of the particulars. Now if the game felt the need to show the woman was still a man visually, by doing something like body swapping during the sex scene, that would start getting gay pretty quick. Why? Because now it's two men having sex. It was two men having sex before you might say, but visually, it wasn't.
I think if I suddenly found myself in a woman's body, I'd just be a 'lesbian.' Assuming my brain stays pretty much the same in the process, I just don't find men sexually attractive. Even if I knew that there would be some amount of pleasure to be had having sex with a man at that point, I don't think I could make the mental leap. At the same time, I'm perfectly happy to make a fictional character do it. The same way I could make a game character shoot an innocent person in the head while they beg for their life. I don't think that makes me some kind of psychopath and I don't think making a transformed dude perform sex acts make me gay.
Additional thought: I think a transformation game would put me off if we are constantly reminded that the transformed character really doesn't want to do these things. Though the same would be said of any corruption style game. If the woman doesn't become corrupted (begin to enjoy it) then it sucks all the fun out of it as well.