Yeah, so, I don't know if that's what you were looking for, but I have some personal input on this. First of all, I could genuinely see them being t4t, you're so right. It's not a set in stone headcanon for me, but I like it.
So, the fun thing is, I actually figured that I am in fact a trans man while watching Gotham. To me Oswald was probably the first character who I could relate to so closely, because his story could easily be applied to mtf experiences.
The biggest thing for me probably was Oswald not being seen as a threat or taken seriously as well as other characters feeling justified to say things about Penguin's appearance, mental state and how he's perceived as an insult once he fucks up (for example, the scene with Gabe, before Penguin lashes out and murders the guy). I've experienced this a lot personally, those low blows out of nowhere after an unrelated mistake are very real.
Oswald is also very queer in his mannerisms and behaviour. Not necessarily feminine, but not exactly like the rest of the men in the show either. Especially compared to someone like Jim the straight man™. And this could be applied to older Penguin as well, because I know for sure if I didn't force myself to battle my insecurities, I would've also been a mean, bitter piece of shit after a while. Feeling disfigured or freakish is something that I've personally struggled with.
Riddler though just gives off trans vibes. Which way? Oh, well, that's a riddle. Could be anything at this point, lol. Also, I just want to throw it in, why didn't Riddler appear in any of the pride collection stuff, despite already being pretty much confirmed to be bi in the comics?
I find it so confusing honestly, but I feel like dc are just being cowardly with their villains being out and proud. Because Ivy and Harley as a pair are marketed as anti-heroes/vigilantes. It's probably the "good representation" problem all over again. I understand historical implications of queerness being villainized in media, but it could be done right. Being gay or trans shouldn't be a privilege reserved only for "the good ones"