This can alienate the 8.3%+, and is probably one of the reasons why that percentage is that low.
This change isn't just about trans people, but about anyone who doesn't use he/him or isn't male.
That "probably" there isn't justified, in my opinion. As others in that FAQ thread have pointed out, StackOverflow isn't a place where a lot of third-person interaction is taking place, so I'd consider it a stretch to make that out as a reason that non-males are lacking there.
Maybe it's just that women often have better things to do than to ask strangers for help on why their Haskell state monad is acting up.
A new user will typically arrive at SE for asking or answering specific questions. Even most of the users with accounts rarely seem to go near meta and chat.
When I was active on SE (I gave up logging in a few years ago), meta was the afterthought to bitch about some policy or detail and the annoying habits of questioners. The chat usually empty or quiet enough that even looking to see if it was active seemed mostly pointless. I'm sure it's grown since, but that's not really where new people are going.
People are making a huge deal out of nothing.
For 99% of questions and answers pronouns are irrelevant, and rarely ever seen.