It was meant to be colorful language. Again, it's kinda a weird pick to nit. Even if I said yes, I could also say we're still finding them. If we were to go by the original story, the box was empty of everything but hope once the evils were unleashed. But it doesn't mean Pandora was able to catalogue them all as they came screaming out, or encountered them all during her lifetime even. The gender box has been opened for quite a while, it's just more recently that western european culture has been willing to examine what came out.
Except, you can run into this in many situations. Replace terminology with other words, like policy, and you just described a lot of groups (very few groups are homogenous, even if they are "single issue" groups). Yes, it is a controversy in some trans circles (apparently not the ones I'm involved in, we must hang out with different people), but that's okay, and allowed. And yes, on some issues you can take sides and offend the other side (i.e. abortion) and not really have any way around it. When it does happen, it sucks, but I point to OldHack's approach as the best standard approach to work with. Deal with the individual, don't worry so much about how unified the group is (or isn't).
(I meant to post this yesterday, ugh)