I think the Title really explains it best, In many cases these are not actually what people mean when they say things but are often the meaning transgender people take from them, due at least in part to people who do actually mean these things as well as general self confidence issues.
I have had several people tell me I look better as a woman then I did as a man. I know I often take that in a negitive way or assume people are just being overly nice or don't want to upset me. The truth is most of the time when people tell me that they actually think I look better. Maybe its because I seem happier and smile more, it might be because I try harder to look my best or any other little thing, perhaps for the first time my general body language and social interaction more closely matches my precived gender and thus it looks better. Regardless I know that for my own emotional well being I really need to start taking statements like that as the compliments people mean them to be not as back handed attacks.
Serena