There's this weird game from a while back that didn't get much hype.
You'll find it either as "The Experiment" or "Experience112". Got some interesting mechanics, which later influenced another niche game I just realized has a female protagonist: Republique.
Technically, you don't play as a female protagonist. But you're essentially not the main character and you have no discernible physical features anyway, so you could just apply whatever gender you want to whoever you think "your character" is.
It's kind of like... "Female protagonist by proxy". I feel like that's a decent description. The point is that the main character is a (generally) well-written lady protag.