There's also Chattel Religionism, which some time after adopting, has a Council to determine exactly what virtues and focuses the religion will take. And while you could easily make a religion that beatifies slave-owners that have massive stables of groveling slaves, it is equally possible to form a religion that sees comfortable, educated, and trusting slaves as the pinnacle of virtue.The answer to most of this besides the events that play where it's sometimes unavoidable, the player can always just opt into Paternalism, which seems to be pretty easy to get if all of your slaves are educated and happy. I didn't adopt it yet, but mine always says it's primed because only the fresh slaves are actually anything lower than devoted. You get a few events (and some alternate ones) where your Society option basically babies them. The descriptors just for the arcology even describes slaves as being precious and they deserve all the headpats, and it usually carries an air of some misguided utopia. Being a slave is actually better than fending for yourself out in the slowly dying world.
So yeah, anything offensive is mostly the players fault for not reading the fine print I guess.
Mix that with Paternalism, and you basically have slavery as little more than a formality, with the slave-owner being basically just an anchor point for the slaves to safely return to in their daily lives.