The first is that trans women do not have a big advantage over cis women. They have, at best, a very slight advantage, depending on their time on HRT and age.
The second is that there isn't a lot of trans people. Trans people make up around 2-3% of the population, so they would have around 1/30th of the number of teammates in their school. That would be difficult to make a full team around. And because they're segregated out, they would need to find other teams to play against, as well.
The third thing you're missing is that you really only care about trans women in this debate. Do you care if trans men compete against cis men? They compete at very similar levels, too, and if you think being born as a woman is a disadvantage, then why do they do just as well after transitioning?
And the last thing is that we have gendered leagues due to a sexist history behind sports. Women weren't allowed to compete in a variety of sports for a long time. Women's leagues were initially created for the same reason black leagues were created. We have kept them because they are a really lazy way to determine what category of play you are in, as though they act similar to weight classes in wrestling. But athletes within the same sex can compete at completely different abilities for different reasons. Taller players can have a much bigger advantage against shorter players in a ton of sports, so why don't we use height as a determiner of which league you play in instead?
So, any woman with a double mastectomy is no longer a woman? Damn, cancer keeps getting harder and harder.