Was Semenya modifying her body?
In order to compete she was required to take medication that would reduce her natural testosterone levels which would therefore be body modifying. So I guess the answer is yes.
As already stated, the trans approach seems more analogous to drug cheats.
Actually in the cases of both Semenya and trans women athletes it seems to be the exact opposite of a drugs cheat. A drugs cheat takes a substance to enhance their performance above a level that would occur naturally. For Semenya and trans women athletes they are taking a substance to reduce their performance to a lower level than that which would occur naturally.
Do you support Hubbard's participation?
I think it is a minefield and I'm glad I'm not making the decisions. But I do think that the issue of trans women (note just trans women) being able to compete in athletics tournaments for women is distinct from the more general issues of trans rights, specifically because it is about athletic performance.