Calling a comment transphobic in no way implies that the speaker of that comment is transhpobic. It is a description of what's been said. The same way if someone was to say something that could possibly be construed as racist. If someone points that out and says hey that statement is racist, that's not calling that person racist. They might be. They might not, but that statement in and of itself implies no assertion on that actual person.
In short, calling the statement in question transphobic is correct.
How silly it sounds to anthropomorphize the question that way should tell you that you are wrong in this case. A question doesn't have a brain to be ignorant with, nor does it have intentions of any sort: once someone has written it down, it just is.
In TDD, do we talk about a unit test succeeding because I intended for it to fail and it did? No, we say it failed because the actual result is red. I didn't fail, but the test sure did.
Intention doesn't change the impact of communication; if the intent doesn't match the actual outcome, what it means is that the author probably wanted to change it.
In short, calling the statement in question transphobic is correct.