Your two issues are issues because, even without any prejudice, there are physical differences that we have to handle and it's not easy to figure out how to be fair to all parties.
In the case we're talking about, for example, the trans women fractured a woman's skull. Broke her skull. Was the skull the problem here? Should it have been less breakable to match the rhetoric?
Fox fractured her opponent's orbital. This is a facial fracture, not a skull fracture. Skull fractures are life threatening whereas facial fractures generally are not.
There is a large discrepancy in the force required to cause a facial vs skull fracture as well.
MMA is a violent sport. There are risks to anyone participating in it. If you are seriously worried about protecting athletes, there should be more widespread changes than just eliminating the handful of transgender athletes because I guarantee the majority of injuries occur in matches between two cisgender athletes.
If the front line of the battle is people being assholes about pronouns and transgender women competing in combat sports... maybe the war is won?
To clarify: would you argue that the existence of separate drinking fountains for white people and black people is justified because many white people feel uncomfortable drinking from the same fountain a black person has just used? If not, why not?