Like, there are obviously strong and not-particularly-positive feelings involved there yet Breq still feels very protective of Seivarden and Seivarden eventually feels the same way about Breq.

I think what binds them is their history, not necessarily with each other but in general. They're both misfits, and they're the only two in the universe (except for other old ships) that remember the time/cultural milieu in which they were more themselves. That's a bond, even if it's not an easy or acknowledged one. (Incidentally, I love that not only are there different cultures in different parts of the empire, but the cultures change over time, which is one reason Seivarden has such difficulty reintegrating into Radchaai society.)

Also, from Breq's POV, Seivarden was one of her officers; even if she didn't think much of him, I guess that might be why she has residual protective instincts.

I experienced Anaander as female, and I liked how the pronouns caused a kind of dissonance in my reading, where one part of my brain kept poking character discriptions going "man or woman?" and another part of my brain would respond "shhhh, not relevant."