I think many of us were confused because of the rigid and backwards impression we were given by Sten in DA:O and by all the Qunari in DA2. They seemed so cut and dry, so all or nothing (I mean you can't even have sex for love, you get "reprogrammed" for that right?). A person can't choose their job under the Qun, even if they would rather be something else, it seems like "choosing" to be a different gender is more extreme and would have been even less accepted, especially if the biological female was better at something else than she was at fighting (can she not become an aqun athlok in such a case? What if she wants to live as a man but doesn't want to be a soldier?). I definitely got the impression that personal desires didn't matter and "the will of the Qun" was everything. I mean Ketojan killed himself without question even though he didn't want to die because that's what the Qun required
. Sten doesn't even seem to be able to comprehend that a biological female can fight. It would have been less confusing if he had assumed she was transgender. "oh you're an aqun athlok" rather than arguing in confused circles about how women can't fight. I hope this doesn't come across as aggressive or something weird, just trying to explain where my disconnect at least is coming from.
(I don't know about others)
Sten certainly gives us a glimpse of the QUN, but it is "his" interpretation. He's singular in purpose, but not a mindless drone.
DA2 - again, we get a group of Qunari that are tightly and rigidly controlled by the Aristock, but it's "his" interpretation that is paramount. Likely due to circumstances.
Iron Bull - still believes, but his circumstances require that he be more flexible. It's only after the inquisitors influence that makes or breaks his beliefs.
My impression is that only "troublemakers" go to reeducation camps. The warrior cast, our primary exposure to the qunari and the Qun, are trained from an early age, disciplined and ridged, because you don't want a bunch of "touchy feely sensitive dudes" holding the line.