Considering I don’t get to see any of those quests, my suspicion about Kel’thuzad specifically is that some sort of shenanigans were involved. I mean, we didn’t even destroy his phylactery last time we took him down, so he shouldn’t even be in the Shadowlands as far as we know.
In general though, this is my main problem with Maldraxxus. Apparently Blizzard came at it from this perspective:
Another aspect was to play with players’ expectations, as Maldraxxus’ aggressive and evil-looking exterior initially belies its noble purpose, but this also caused the team to worry—at least until the first external playthroughs of the zone started—if players would be able to care and empathize with the characters in such an alien-looking place.
I’m totally okay empathizing with the good guys in Maldraxxus, it just seems like they’re hilariously hard to find. Even the remaining “good” House gets betrayed and taken over by bad guys by the end of the leveling, leaving all Houses either gone or in service to the Jailer.
Worse, it’s all willing. In Bastion, it’s said that most of the Forsworn don’t know who they’re actually working for (and their concerns are entirely valid), in Ardenweald, the bad Night Fae explicitly and tragically have their free will stolen, and even in Revendreth, it’s made clear that most of the Venthyr don’t know their leader is corrupt, and most of them would not stand for it if they realized it was happening (or thought they had a chance to challenge an Eternal One).
As soon as you enter Maldraxxus, however, the bad Margraves admit that all they needed to be told to turn bad was basically “You don’t really care who you’re killing as long as you’re doing it, right?”
I’m not really surprised though. It’s more or less the same problem we have with “oh no, another Horde leader has gone bad”. They want to subvert expectations, that these brutal barbarians with traditionally evil symbolism can actually be good, and there’s a good message there. But someone on the team doesn’t seem to be able to help themselves, and if they’re writing an undead character or a bloodthirsty barbarian, they inevitably slip into tradition. Eventually someone realizes that direction has gone too far, the story has to insist most characters don’t endorse it and blame it on the leader, but the cycle starts over sooner or later.
Because I really can’t help but notice that the “realm that borrows the most evil symbolism but really is good underneath” is nevertheless the one that really does have the most openly malicious characters (and frankly, even the “good” characters don’t seem to have a problem with the Brokers kidnapping people for them to fight, performing horrific experiments on unwilling subjects, or creating biological weapons of mass destruction, and I didn’t see any attempt to prove how that helps them defend the Shadowlands except in the vaguest sense of ‘it makes them stronger’).