Lol "Manly McDragon."
Yes, that was helpful, thanks.
Unfortunately in this case, the aqun-athlok is presented as a concept in regard to Krem, who is trans, so it's a bit difficult to separate the two. Your remark that, "if they'd decided Bull would make a good tamassran instead of a spy," makes the Qun seem a lot more flexible than it appears, particularly as Sten presents it to the player.
However, I will say that that view does make a lot of sense. Let's say that you noticed a child is highly analytical and mentally organized. Obviously, you might want to train that child to do work in maintaining the Qunari breeding program. But this child is "male," and that is a "woman's" role. What to do? Well, if that child is going to be trained in that role because their natural abilities are a match for it, then they are a "woman." As Fenris tells us, the Qunari waste nothing, so I wouldn't be surprised if they went through some mental gymnastics to have their cake and eat it too in regard to gender roles. But I do wish it had been presented in that way, rather than as a way that enabled Bull to be accepting of Krem, or Cassandra, or hell, even a fem warrior Inquisitor.
Now, I'm not one of those to cry "retcon!" when new things are presented that might not completely jive with my previous view of something, but I do think it is one failing of the Dragon Age method of presenting cultures so subjectively, even going as far as having a majority of the codex presented subjectively. Or, you could look at that as a benefit, since it makes the setting seem more real for our character. They only really know what is presented to them, and in this case, the PC's primary interaction with Qunari is through Iron Bull.
Glad I could help!
As far as 'mental gymnastics to have their cake and eat it too' - that is precisely right! As Gaider said, "it involves a weird sort of willful ignorance thing the Qunari are very good at." If a mage is basalit-an, they're not really a mage. They're just a worthy opponent who happens to have phenomenal cosmic power.
shrruuuuug
In its own way, the Qun is incredibly flexible. Bull's entry in WoT2 is rife with this. After he suffers his breakdown in Seheron, he turns himself into the reeducators so that he may be "repaired or destroyed". The Qunari waste nothing. The book says, "Hissrad's mind remained sharp--too sharp, in fact, for the treacherous island of Seheron, where it could so easily shatter. He would be dangerous as a police agent, defiant as a soldier, and wasted as a laborer." So it's not without precedent for those in charge to say... 'you know what, this role doesn't suit you after all, THIS is who you truly are. Nope, don't question it, we know what we're doing this time. Sshhhh.' According the that line of thought, the Qun is perfect but people are imperfect, so when you get fitted to the "wrong" role it's not because the Qun is flawed... it's 'cause your tamassran screwed up when she decided you'd be a great dogwalker.
Sten and the Arishok both make it clear that they're in no position to explain the Qun to anyone. Another sign of Bull's inclinations. He has no problem trying to explain things that are explicitly
not within his jurisdiction to explain. He's not a tamassran, so according to the Qun he has no business labeling Krem or anyone else aqun-athlok. But he wants to, because he believes one thing in his heart and needs to tell himself that his thoughts align with the Qun.
And yeah, it's all a bit of a subjective mess.

Like when spirits (or are they demons?) and abominations (is that the same thing as being possessed?) come up. Bunch of stuff we have to interpret through the cultural lens of the characters who reside in this world.