Thats just the way the game responds to your actions. Like for instance if you recruit the mages but don't send the Chargers to Therinfall Redoubt then you never see or hear about the Envy Demon
I might be mistaken but you get to learn about Envy Demon in Cassndra's quest.
At any rate the so called alliance Qunari are proposing is not an alliance between equal partners, it's an alliance on their terms. The way I see it there are many benefit to not ally yourself with Qunari (you get to know who were Qunari spies for instance).
It seems like the Qunari hold the Inquisitor in high esteem during the Qunari alliance, which is mentioned by Tallis. It also seems like Tallis or Iron Bull may be the next Arquin.
Ben-Hassrath is a role under the Qun, if you listen to IB it means "liar" and IB indirectly implies that the title is not all that flattering and from what I'm reading on wiki "Basalit-an" is a worthy foe, that's one really peculiar way to view someone you ally.
I know it only happens when you ally with the Qunari, but I can't imagine why it wouldn't happen otherwise.
Because it's a test, because this quest is also about hardening/softening IB, if you ally yourself with Qun, IB will eventually betray you, because his first loyalty will be to Qun, if not - he will turn away from Qun for good.
Letting Iron Bull join the inquisition in the first place is a huge mistake. The guy said outright that he's a spy and a good one at that. Talking to Iron bull shows you that he's real good at reading people.
Keep you friends close, but your enemies closer.