My thoughts on the Aqun-Athlok concept:
I feel like their intention with the Tamassrans being at one's beck and call for sex and the Aqun-Athlok was to make the Qun seem more relatable and accepting but IMO it backfired. You have the whole sex-slave thing with Tamassrans and with the Aqun-Athlok, it seems fine at first because it fits Krem's situation: he identifies as male and is a good warrior but it really just doesn't make any sense. For one, they're not actually accepting of transgender identity. If you have someone who is biologically male though identifies as female but their greatest skill is being a warrior then tough cookies, you're a man no matter how you think of yourself. If you're biologically female and think of yourself as female (and even have the handy dandy ability to become pregnant) but are a skilled warrior then you're relabeled as a man no matter how you think of yourself. You'll look the same, feel the same way about yourself, but have a different label forced on you. So clearly it's not about the emotion based choice of respecting people's gender identity but it's also not logical. A cold but logical gender discrimination would forbid women from fighting because since a woman can only give birth once every 9 months but a man can impregnate multiple women without the same kind of limits women would be more reproductively valuable and therefore kept as safe as possible.
The Qun as it was presented in DA:O and DA2 seemed to follow the latter. It's not appealing to most of us in modern society as it takes away individuality and freedom but it was at least logical. The Qun as it's presented in DA:I makes no sense and seems to contradict itself. "Women can't fight but some women can fight so instead of making exceptions and letting women fight we forbid women from fighting but let women fight and just call them men,"
wut. We're also clearly told even in DA:I about reprograming people who stray from their assigned role and yet if Iron Bull chooses to warn the Chargers instead of letting them die, he may have done something that hurts the Qun but is clearly not actively rebellious against it and yet they never try to bring him back for "re-education." This kind of slip up seems like the perfect example of someone who needs to be re-educated as he's not rebellious and was a great asset but is emotionally compromised and confused and has been left with too much freedom for too long. Instead of following their own logic though, they just immediately shut him out and try to kill him.
I never liked the Qun but I enjoyed it as an alien and antagonistic force. It was something so cold and logical but there were also good points such as lack of crime, poverty, roles assigned based on abilities rather than certain races or social classes never being able to rise above and so on. You had the utterly horrifying treatment of mages and yet the Qunari didn't have abominations, demons, and blood mages running rampant because of it. It was horrible and yet you could see how desperate people such as runaway slaves and the poor and oppressed might find it better than what they had. The Qun now...it just seems like a bunch of random ideas made up on the spot and kind of thrown together to make something that just doesn't seem well realized or believable. I can't imagine it as a real culture.
I feel like the ideas of casual sex and acceptance of gender identity shouldn't have been shoved in to try and make the Qun seem more relatable, they should have been Iron Bull's traits. I think it would have helped the Qun as a concept stay logical but also made Iron Bull's struggle between the rigid Qun and the more modern rest of Thedas seem more moving, more personal.
I think you've missed the most important undertone to the IB discussing the Qun: he thinks it's an awful system. He's not lauding its virtues when he talks about it - he's highlighting its horror. He's funny and jovial and people seem unable to actually parse his meaning because of it. But he's not.
The Qun was NEVER logical. It is insane troll logic and logical fallacies through and through. This comes from some of the very first conversations we have with Sten. The Arishok goes even further in illustrating the absurd and abusive hypocrisy of the Qun.
The Qun doesn't assign roles based on your ability. It defines you as a person based on what a small cadre of elite decide defines your ability. This is the point that's driven home by the Arishok and the Saarebas in DA2, and we see with Sten in DAO. It's not a virtue - the Qunari just portray it that way, in the same way that Dorian gives you his slavery isn't all that bad speech.
The Qun just isn't logical. Hawke can ask the Arishok how many qunari he lost to the Tal-vasoth. The response is that he lost none - because a "true" Qunari would never do it. That's not logic -that's the No True Scotsman logical fallacy. The most basic idea of the Qun is nonsense.
The Qun is a strange and alien set of presumptions that are totally divorced from reality and applied in an ad hoc and self serving way. It's been this way since DAO.
What we learn about the Qun in DAI is just more reality denying logic - it's a syllogism that works only on insane troll logic.
As for re-education, you're missing the point. The IB was already re-educated. It failed. Everything about his story is about his trying to own up to the fact that he's already abandoned the Qun. He just can't get himself to own up to it until he has to actually abandon it to save the Chargers. That's why he breaks the moment they're sacrificed.
Every single thing he says about the Qun emphasizes how awful he views it to be - everything he says about Seheron and Par Vollen stresses how broken the society is