She is, yes! (This is also something that comes up in her first appearance in Opportunity). As for how it affects the story, I'll say that while this isn't going to be a story "about" Sasha being trans, it will come up from time to time (as will other parts of her background).
Viewing post in Monstrous Liberation Prologue comments
There really isn't much in the way of narrative overlap - you don't HAVE to play Opportunity to enjoy MonLib by any means (although obviously I think it's good). Sasha just made sense as a protagonist when we were in the early stages of planning for MonLib, so we thought it'd be neat to have that little bit of connective tissue between the games.