What do you mean by “doing something special” if not treating the trans man as a man and trans woman as a woman? If you are more specific maybe I can try to clarify why people might have thought it was transphobic.

I mean pretty much just that in the general sense. I'm not sure where the confusion about this rose from. Perhaps from the context of some sports, where drawing the line is not this easy?

And for the record I tend to agree with flyingsquid from the linked thread- definitions should be rigorous and accurately/comprehensively describe reality.

Agreed. Difference is that I think the biological definition describes reality very well, even if not perfectly. It doesn't seem to me that any competing definition is doing a better job.

But it's perfectly fine not to 100% agree about this. It's the insinuation (that I might be imagining) of being evil that's disturbing.