I don't think the line is intended as transphobic. Sera is above all thoughtless: she doesn't think about the consequences of her actions or take the feelings of others into consideration (especially Elves and their religious beliefs). She lists a bunch of things that people would want to keep secret (stds, illegitimate child, etc.) and includes 'he is a she' in there as though it were shameful/bad/whatever.
I don't think that's how she meant it though. Sera likes one thing above all: to knock nobles off their pedestal. So she points out they're 'not so great' by revealing they have a disease, an illegitimate child, etc. I don't think it's Sera who has a problem with that. It's the people themselves, and she's using that to get to them, because they're nobles. She doesn't think beyond that. To her nobles are not really people so she doesn't care how sensitive an issue something is to someone.
TL;DR: Sera has no brain to mouth filter. 