Actually, with many transgenders, neither science nor evolution said that they were a woman/man. Many of them do not have XY chromosomes. Instead, they have XXXY, XXXX, XXXXXY, XXXXXX, etc. IOW, they have genetic abnormalities that play with not only their sex organs, but their minds as well. 
it is from this that we get hermaphrodites. In addition, you will find ppl that have ovaries and penis, amongst other interesting issues such as 2 vagina, or 2 penis. 
For these ppl, their minds can really be having a difficult time reconciling what to do, esp, with our culture.