I just finished this quest and didn't experience any of all the things you've mentioned because the moment I sneaked my way in I decided I wasn't going to fight my way through it. Left, went to Sorcerous Soundries to pick up a few things and came back with only my bard.
Chugged an invisibility potion and floated my drow ass through the first and 2nd floor with the Fly illithid power. Pickpocketed the guy to get the key, used a scroll of greater invisibility and placed the bomb. Cutscene triggered and I was out in less than 5 minutes.
I imagine that in-universe my bard did this whole thing without even telling her companions who may have disapproved. They were probably drinking ale at the Elfsong when they heard the big BOOM, lol.
