I completely agree. I know and have worked with many people who communicate that way. I'd probably prefer it if they didn't, but I also don't generally have a problem when they do. I would feel that the explanation was unnecessarily pedantic and perhaps the slightest bit disrespectful in its assumption that I didn't know what I was talking about, but I would assume that was unintentional. It's interesting that the reaction from this data scientist individual came back so extremely negative.

The more I think of it, this whole thing is like something out of Portlandia.

https://en.wikipedia.org/wiki/Portlandia_(TV_series)

It's not irrelevant because it's the reason she was fired, and hence the reason the post exists. The fact that you disagree with her assertion about the question seems to be the irrelevant thing to me.

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.