On the topic of whether Varis's overtures are trustworthy, I don't feel like the Emperor should be expected to personally appeal his case. That's what ambassadors are FOR. For the Emperor to make a personal appearance is a ridiculous and unnecessary risk. He's an INCREDIBLE target of opportunity. I still feel that his personal appearance in the Sea of Clouds was kind of silly, and barely justified by the fact that it was unexpected and in a place where foes were sparse (Ishgard was, at that point, neutral as far as Garlean relations went). For Varis himself to personally meet with an enemy with whom his nation is at open war, he'd need to bring a ridiculously large force of guards - and at that point, it'd be foolishly dangerous for us to meet with them. No, sending an ambassador is not an indication that Varis is taking the alliance lightly.

However, I do think that the possibility is still strong that Varis is setting a trap. While Zenos might have been a "failed experiment", it's uncertain that the Resonance was. If Aulus's findings were shared with the Empire, Varis might well consider us to now be expendable. Even if Resonance has side effects, it still produced individuals like Fordola, who was extremely formidable. The Empire almost certainly doesn't know about her "forced Echo" fits - and even if they did, I'm sure they could dredge up soldiers with a lot less empathy than she has. After all, she's only suffering because she feels guilty about the atrocities she perpetrated and was now forced to relive from the perspective of her victims; a sociopath wouldn't have that weakness.

Basically, Varis might consider the Resonance to be "good enough", and is now set to take out his most formidable enemy: the Warrior of Light.

On the topic of Yotsuyu, I don't think we have enough information to place the blame for her situation at the feet of Doman law, or even of Doman custom. We don't really know how legal or customary her treatment was. Certainly it's the case that even in real-world, civilized nations, some families will sell their children into prostitution even though it's far from legal or customary. The fact that Yotsuyu DID decide to enact vengeance on Domans in general hints that it's a known and tolerated phenomenon - but it could just as easily be the case that there's little logic in how she chose to lash out. She wanted to see people suffer, just as she had suffered, and Domans were a convenient target.

Honestly, though, that Yotsuyu is dead, so the debate is of little importance. As for Yotsuyu now, I doubt that she's faking her amnesia, and I'm interested to see what interactions she'll have with Asahi, a ghost from her past, when most of her past is now gone. If she's regressed to childhood, was she on good terms with her cousin before she was sold off for his benefit? And on Asahi's part, does he feel any guilt for the way that his high position was gained by trampling on his cousin? If he does feel guilty, and comes face to face with Yotsuyu when she was still young and trusting, it could be interesting indeed...