There's a link above where David Gaider talks quite a bit about how they conceptualize the aqun-athlok in the Qun. It appears it's not "friendly and accepting", because it's not something you choose for yourself. It's not a situation where a person comes to their own conclusion about their own gender identity and it's just immediately respected. From Gaider's explanation, my impression is that the Tamassran decide for you. Thus, some people would be declared aqun-athlok just because their skills lean a certain way, while some that feel they should be would not be accepted as such.
And see, what I'm saying is it's probably even more horrifying than just that, when you get right down to it. Think about it from a real world perspective: I'm a guy, both in terms of biology and identity, and I work in education, so my "role" in the Qun might actually be similar to that of a Tamassran. So if the Qunari conquered real life, I'd have to be a "woman". But as it's presented by Bull, the "woman" designation wouldn't be anything other than a differing set of pronouns that would take a little while to get used to, sure, but would be ultimately meaningless, since my role decides my gender, rather than vice-versa. Basically, the "it would suck for people who identify as their biological gender to be given a non-biologically-appropriate role" argument is basically null and void because gender is meaningless under the Qun outside of role anyway.
Of course, I like I said, I doubt it really
is as simple as that. Perhaps literal mutilation is involved to get your body "in line" with your gender? I wouldn't put it past the Qunari to do something like that. The point is that, whether deliberately or simply unconsciously, Bull seems to avoid mentioning the more unpleasant side of the whole truth when he talks about the Qun.
Similarly,
because sex is considered a factor in determination of roles, I honestly doubt Aqun-Athlok are even really a thing the Qunari commonly handle or know how to deal with. Like you said, the Tamassrans decide everything, so if "women can't be soldiers", they're not going to raise biologically female children to handle "male" roles. Even when children naturally present talents, those talents will be pushed towards appropriate-gendered roles that they apply to. A female who shows a proclivity for fighting, for example, would be put in the Ben Hassrath rather than the Antaam. It's different, of course, with conquered individuals (like Krem, or better yet for this example, let's say Aveline) who have both talent and experience in an "inappropriate" field, and for whom re-education is less efficient than the reassignment of a potentially-meaningless binary value.