I think you have a point, and of course no one study is going to be perfect. At the same time though one of the major strengths of this study is that it looked at large numbers of both MtF and FtM patients, and the results seem consistent, with both MtF and FtM sharing similar outcomes. If FFS was the key variable that was being ignored then you'd expect to see a stark difference between those populations.

The mean ages of participants also trended young, mostly still in their teens, which means that quite a few of the participants were receiving treatment before or during early puberty.