You're right, but limited representation is a problem. Basically, when you're given a single source with no additional information that would damage source's credibility, you can assume that you're getting relatively good insight into the topic covered. Obvioulsy Sten could be biased and Iron Bull could be just lying in Krem's face, in fact every single piece of information can be questioned and most of them discarded as we usually don't get more than one source for most things - if we approached the lore with scrutiny appropriate for real-life problems we wouldn't have too much left. But the thing is that - unlike in real life - we're generally unable to look for more reliable (or just different) sources. As with other works of fiction, we're forced to accept sources given or discard pretty much everything we know about Thedas as unreliable. That's where kind of informal "deal" between writers and readers is struck - readers take what they hear/read/see at face value to greater extent than they would in real life while writers don't have to give a couple reliable sources for every detail to introduce it as part of the world.
Therefore when faced with accounts that aren't implied to be unreliable, players generally assume that even including some bias coming from in-game author of information they're generally told the truth, and the more knowledgeable the source seems to be, the more they can believe it, perhaps distrusting interpretation but not really the facts.
Obviously, some accounts are proven to be wrong, but when some element was introduced by a source that seemed reliable, knowledgeable AND uncontested (there wasn't reallya ny source other than Sten to learn about Qun), its account was understandably taken as binding, since there was completely no reason for Player to doubt it. Suddenly departing from that account in significant manner combined with lots of semantic play to "prove" that there isn't any change, really, it all fits... Well, it leaves people with bad taste in their mouth. Because it's like the writers try and weasel out of their side of the deal I mentioned - deal that is really indispensable for purposes of building a rich world through interaction with a bunch of NPC plus written in-world codex entries.
On the topic of the Qun - and I was hoping to avoid a substantive debate on this point to not necessarily derail the thread - I think people really fail to appreciate just how much the whole religion works on insane troll logic. Let's use the Arishok as an example in DA2. When you talk to him about the tal-vasoth, Hawke says (at some point): "How many qunari have you lost to the Tal-Vasoth?" The reply from the Arishok is "None." This answer is, of course, idiotic nonsense. Every single tal-vasoth plaguing Kirkwall is a qunari desserter. And yet the Arikshok - by using the No True Scotsman logical fallacy - honestly believes his answer to be true, and the Qun would likely demand that answer.
When Sten talks about women, he's talking about notional categories in the Qun that sort of map on to the concepts as we (and the rest of Thedas) understand them, but not directly. In the same way that a qunari deserter was "never" a qunari, but always a tal-vasoth, a warrior was always a man, never a woman.
What breaks Sten's mind is that the equivalent of the Tal-Vasoth saying "I am a qunari." It's nonsense on the internal troll logic standard, which works as a twisted form of modus tollens and ponens working from nutty premises.
On the topic of the setting - I agree that there is an issue with people assuming that the one character they speak with is an authority on the setting, because they're the only informational source. But I am not sure that is really an issue with the writer so much as it is with the audience. We are so used to have omniscient perspectives in novels and written media that we are not appropriately skeptical about authors and the information that they give us.