I agree with so many points about Cassandra and butch/masc girls in (Bioware) games. It's definitely a complex topic.
As a butch queer girl myself it's really frustrating every time a masculine girl is revealed to be straight, in part because they say it's inverting stereotypes or whatever... Not to say there aren't masculine straight women but... I dunno. It makes me tired.
I don't really know of any games that do have specifically queer butch girls... I would love to find some to add to my wishlist or download, though, cause I wanna see NPCs and protagonists who are like, maybe sort of like me.
I really like Emily Kaldwin from Dishonored 2 but I'm not sure she entirely... fits the bill? Nebulous. Tracer I think counts, she's got some soft butch vibes, but multiplayer games make me anxious lol
I also share a lot of the mixed feelings as other people wrt Bioware. I really like Mass Effect but I have a lot of conflicting feelings about the game, from a queer girl perspective and also from a queer girl who likes character design perspective.
As far as games and butch rep go, in fairness I can't know every game there is, and I'm sure they are out there especially in the indie scene. Queerly Represent Me has been helpful for finding queer games in general, both indie and less-indie but it's a little tough to navigate for me, since it's in list form.
Also, people noted Read Only Memories above and I downloaded the 2064 demo and played it this week and it was really nice to be able to choose from such a variety of pronouns! I wish more games (Sims 4...) (also all games) would do that. Plus it has cute art which is always a plus.