To me there seems to be two simple solutions to this problem.
Firstly, the existence of sex-separated sports is inherently acknowledging that there are differences between sexes and that there is a belief that for one reason or another, males and females should be separated in competition.
If you are born a female, you should be competing against females, because regardless of what you identify as, you have the physiology of the female sex, and visa versa.
If you are born a female and undergoing therapy to become a male, first and foremost it needs to be determined if this therapy is within whatever banned PED testing goes on in sport. If the therapy falls within the definition of something that is banned from use, one simple solution is that you should not be allowed to compete period.
A second, more lenient solution would be that there be an analysis of sex-change therapies to judge whether or not a female undergoing therapy to become a male is
1. based on the criteria by which "males and females should be separated in competition", more fit to compete against males rather than females.
2. This therapy does not give a female transitioning to a male an unfair advantage against natural males.
If those criteria are met, then a female transitioning to a male should be allowed to compete against males.
Same would apply in the alternate condition. Then it comes down to really defining why "males and females should be separated in competition." If hypothetically males are inherently better at a given sport than females, and the reason for separation of sexes is to give females a platform to compete amongst females, then a male transitioning to a female would not satisfy condition 1, in that she would not be more fit to compete against females than males.
