Same with the Qun, they wanted a transgender in the game, and the easiest way to explain it in a medieval setting like Thedas is to atribute this "deviancy from the norm" to how progressive Qun is. Lore? An afterthought.
People, no. The Qun is not progressive for having a term for transgender people. That's the whole problem with this thread - everyone seems to assume this is automatically "progressive" and "liberal" and "modern." It's not.
There is nothing inherently progressive about not determining someone's societal gender based on physical primary and secondary sex characteristics. The Qun evidently views gender identity as something that is formed in the mind: yes, this matches our own modern scientific viewpoint*, no that is not incompatible with a rigid and regressive societal structure with clearly defined gender roles.
As countless people have already pointed out, Sten's confusion regarding a female Warden fighting has to do with the fact that she considers herself a woman. The Iron Bull tells us that there is a term for people who consider themselves men and fill that societal role. Bioware hasn't retconned anything - the writers filled a gap in the lore, because before, we didn't know if there was a term for what Sten thought the Warden was. What's more, even if this were a retcon, it would be one that makes anthropological sense, because real-world societies with rigidly defined gender roles often have rigidly defined exceptions as well.
The Qun still doesn't allow self-identified women to fill the societal roles of men, or self-identified men to fill the societal roles of women. Maybe Aqun-Athloks are treated as their self-identified gender 100% of the time (outside of reproduction I guess) or maybe they're treated more like a third gender (which often exist in societies with very strict gender roles!), but the point is they are not treated as the gender that shares their external physical sex characteristics. It still sucks to be a woman under the Qun who wants to fight, or a man under the Qun who wants to trade.
I'm getting really freaked out by people who say that the Qun is being too "nice" about this, and that's why they think it's an undesirable retcon. 1) It's not automatically "nice" to have a different view on what determines gender, 2) even if it was, why are you so invested in the Qun being horrible to the same people the real world is horrible to.
*eg There's a part of the brain, called the BST, that has been linked to androgen and estrogen production, as well as sexual behavior in lab rats. There's evidence that MtF transgender women have a BST sized comparably to cisgender women, while cisgender men's BST is twice as large. This is a statistically significant difference. It couldn't be explained either by sexuality, since both straight and gay men were studied, or by adult hormones, since both trans women who'd undergone surgery and cis men who'd undergone surgery to remove the penis were studied. Ergo, evidence that early brain development of trans women is closer to early brain development of cis women. The study can be found here.