While some of the H-scenes occasionally play around with humiliation as a theme, on the whole this game is pretty much the opposite of "dark." You're not going to see any scenes where Alex (or anyone else) are seriously and in an un-fun way humiliated/degraded/etc.
I do like some of the darker TFGS-type games, but The Proteus Effect is definitely not one of those kind of games.
For the record, the PC isn't necessarily poorly endowed IRL. You set that in one of the early H-scenes, and while "tiny" is one of the options, it certainly isn't the only one.
Maybe one of the scenes will see Alex temporarily become a futa, though. Could be interesting.