Musculoskeletal differences between male and female bodies are more than just hormonal and ephemeral; they are quite literally bone-deep. If someone digs me up two thousand years from now, they won't be able to tell if I took hormones or how I felt about my gender or much of anything else about me, but they will be able to tell that I was biologically a woman from nothing but my bones.
As to whether those differences confer an advantage, I guess that depends on whether longer arms, more massive bone structure and greater upper body strength count as advantages. I would contend they do. If she'd been taking hormones since she hit puberty, then no, she wouldn't have developed those advantages, but her current course of hormones has not undone the development that happened at puberty.
Men wipe the floor with women in sporting events. Even though she doesn't identify as a man and is not a man in any other sense, she retains the physical advantages of the sex she was during puberty when her muscles and bones put on all that extra mass and grew in different ways. It sucks for her, but I don't think she can compete fairly against XX women or against men at this point.