Strange I have had other M2Fs in real life confirm what has happened to me. Just because you haven't met someone that it has happened to doesn't mean it hasn't happened. Your view of the world must be very limited if you will only take things that you have personally seen. I'm also not claiming it happens to everyone, as with all this HRT the effects are extremely varied. But for me one of the unexpected and very welcome consequences was some minor shrinkage. As for toe nail sizes, no they have not changed; as the most likely affected areas seem to be related to cartilage and other connective tissues, as other people keep saying.
However if you want to think about the dimorphic physical differences between males and females, and the evolutionary reasons for them, you can suggest some ideas.
Firstly Males where traditionally the hunter gathers, the reason why men have better depth perception, larger muscles and a more rugged skeleton. Females were meant to bear children and look after them. They remained in a more social situation, in which they developed a very co-dominant brain, lower muscle mass and a smaller more delicate skeleton.
If you have a larger skeleton and a more evolutionary developed physical body, that knows it is male only from the hormones, surely this body would also increase the mass and strength of the cartilage, and connective tissues as well, to be able to withstand the increase fatigue the male body would receive. But as these tissues are soft, and are developed by hormones, the change of hormones could in some individuals cause the soft tissue density and mass to decrease.
Surely that could lead to me now fitting in some lovely shoes and been shorter as a consequence of HRT? Of course all not proved, but the suggestions that people have given you should indicate there is a real possibility that this has and does happen. I just know that it does sometimes as I've seen it on myself and so have others!!
You are trying to disprove something by speculation we are saying it has happened, as it has to us. If you don't believe us fine, we are not putting it out there to be peer reviewed, we are just stating consequences of HRT on us personally.