I think you're being too sensitive here, and also taking the transgender's account as the whole story and assuming it to be 100% accurate. You need to be open to the other side of the story. You don't know who was giving attitude to who first. You don't know the mannerisms and body language that may be been communicated and/or mis-communicated.
I agree the employee should probably have been "sharper" and recognized the sensitive situation.
But this is not a "royal **** up" - it is an oversight that was easy to miss. Yes, it was a mistake nonetheless. Eye-rolling is rude too. Many, if not most people have never encountered such a situation where they are dealing with someone who's ID is radically different from the real person. But I would bet that it started out with an honest double-check from the staff, which lead to questioning, which then lead to more confusion, and then it took a while (too long) and the light bulb went off in the flight staff's head and she suddenly realized "Ohhhhh, I get it now..... its one of those transgender people...... I read all about it in the news but whoa, I've never actually encountered one"