Considering the fact that most women's leagues barely get any mainstream attention as is, I think any further fragmentation of sports isn't going to be sustainable.
Also, ignoring the commercial and entertainment aspect of sports, it's just really hard to organize local leagues if they only serve a small portion of the population. Like, even in a large metropolitan area, how many transgender people are there? Of those, how many are interested in a particular sport? Of those, how many are interested enough to form a club?