I can't believe it is 2016 and "If you are going to write an article about a marginalized group, you should do it in a way that is respectful of them" is something that still needs to be said.
I've come across a number of articles about autism and gender identity, and some of them were not respectful to autistic trans people at all. They called the trans men in the studies they talked about "girls", implied that the solution to autistic trans people's dysphoria is to treat their autism rather than transition, and/or implied that some autistic trans people aren't really trans - just in need of an outlet for gender non-conformity. As an autistic trans man, I felt slapped in the face.
First of all, if you're going to write about a demographic of trans people you should be gendering us correctly. I understand that you might be writing for readers who may not know what "trans man" means, but you can always define the term in the article to minimize reader confusion. Furthermore, when you call us the gender we were assigned at birth, it encourages others to think of us as such. We do not want to be thought of as the gender we were assigned at birth. We want to be thought of as what we identify as. If you refer to us as what we identify as - perhaps with a footnote or something saying what that means - you will encourage other people to do so as well. Journalism that benefits the population it writes about? Now that's what I call ethical!
Secondly, pushing the notion that one's transgender identity must come from nowhere for it to be valid or respectable is very dangerous to the transgender community. Doing so would cause people to believe that our gender identities are up for debate, which would result in them not respecting us until we "prove" how trans we are. We should not have to do that. If I say that I'm a boy and I use he/him pronouns, your response should be "OK, thanks for telling me. I will now use he/him pronouns to refer to you." It should not be "Prove to me that you are trans and only then will I gender you correctly." That being a common response to "My preferred pronouns are [x]" would be an inconvenience to all trans people, autistic or not.
Even more dangerous is the implication that autism can "cause gender confusion" and make cis autistic people mistakenly believe they're trans. I do not like this implication because it could result in autistic trans people having to have a doctor tell them they're Really Transâ„¢ for their family, classmates and/or coworkers to respect them. This is a barrier between us and social acceptance that should not exist. Furthermore, there are countless parents of trans children that do not want their children to be trans. If you give them a thinkpiece with the implication that their transness might be due to their autism, they will use it as an excuse to not accept their child. They will make their child go to therapy thinking that a psychotherapeutic approach will "cure" their child's gender identity -- and that is unacceptable.
I have said it many times in real life and I will say it electronically: one's gender identity is to be respected regardless of where it comes from and how it came to be. Is my gender identity caused by my autism? I don't know, but it is valid either way. To tell me otherwise is ableist and transphobic, and I refuse to accept it.