Jane -
Well yes, the changes post-HRT and post-transition are big and certainly will have an effect, which is why those studies try to look at pre-everything people or try to eliminate adult hormonal influences. I am a scientist, so I am not so much interested in dropping studying a subject for political correctness reasons. If there is a physiological marker, then it does exist. If people take it then in an elitist way, that is an issue that has to be dealt with then, not the fact itself.
So that 12 week mark is what I was wondering about. Consider that for some reason or another there is a time - some days or weeks - in which the XY fetus gets hormones that cause feminization (just as an example now). That time starts at some point and ends at another later point. Now if it starts some days before the 12 week mark and ends sometime later, it would affect body a little bit, brain a lot. This would be the most likely case then actually - more likely than the hormone surge coming only before the 12th week or only after the 12th week and of course the control group are the ones not having any such surge at all. In that case, I would almost guess that quite a few people who got that hormone surge had it in a way that was spanning over some part of the body development as well as the brain development. I know this is a bit dangerous to think about politically as there may be that idiotic idea coming from it that some people are "more legit" than others, but that is nonsense as obviously there will be cases where the surge comes only after the 12th week and thus only brain is affected and that is not less "legit" than anything else. But such a overlapping surge would be quite common then and explain possibly why for some TS people the body is not quite male as well.
AFAIK there is no MRT technique yet available that shows structures that differ between male and female on birth. thinking patterns are just too susceptible to change with life experiences. AFAIK they had to do the analyses post-mortem to get into these differences they are mentioning. Its a bit of a tough subject as obviously it is hard to divide brain structures or patterns that developed before birth from after birth, pre-puberty to adolescence. Learned behaviour adds to that. And certainly does being post-op for many years. Even worse if the data can only be gotten post-mortem.