It encourages stealth too (if you so choose) by providing the chain assassin bonuses etc.
I don’t think there’s anything arcane about the mechanics - are you getting spotted, or leaving bodies lying around? Have you scoped out the area adequately? Use sleep darts? Pick a good ingress point. There’s usually plenty of hiding spots that encourage stealth, and sometimes hidden entrances.
I’ve regularly managed full stealth missions, where I recover the treasures and kill the captains without alerting anyone and getting sucked into melee. And plenty where I have of course! :)