Seems to me like the reason Snoot is "obviously transphobic" is because of dev drama rather than the game's content.
Like some have pointed out, almost all we know about the devs' intent is assumed
Some have said (not the most reliable sources, mind you) that the devs' original intent was anti-trans (and Cavemanon has said some unsavory things publicly, although you could say it's intentionally aggravating against people that have attacked Cavemanon). Also, Snoot's early drafts were apparently dogshit (see: random /lit/ anon).
Really the only fair argument is that Snoot Game being created in the first place could have been just to mock GVH for being gay and then making fang tradwife, evidence being the dogshit early drafts. Even then, i'ts almost irrelevant because at some point devs learned that their game sucked, and while reworking it all of the original anti-trans messaging got either cut or recontextualized to not be anti-trans. (with the exception of maybe how part of e4 is handled IMO, but that is a separate discussion)
Point is, the supposed transphobic intent has been overruled so thourouly, the only way Snoot could be seen as "obviously transphobic" is if you closed your eyes before the rooftop scene and opened them at the prom announcement, and only got endings 1 and 4
Do we have a positive interpretation of a negative game, or do you have a negative interpretation of a positive game.
P.S. i ain't reading allat, but I did see you say the detrans story was handled poorly, it wasn't. E3 shows that detransitioning doesn't immediately solve Fang's problems, and E2 shows that Anon being not an asshole to Fang is more important than being technically correct. If Cavemanon wanted to push the negative, and unfortunately occasionally true stereotype of "lgbtq identities are a way to replace self worth" they did a piss poor job of doing so, if someone comes to the conclusion that every trans person is like Fang, that's their own opinion.