Yep, boss maps all are cleared when you take down the main guy. Presumably, Goblins, Oozes and Death Caps don't wanna mess with someone who beat up a Troll.
All 39 battles were in the Cram Jam version- although I don't know if they'd be winnable, as I just discovered another pretty nasty bug that prevents Eloise from stocking new items after the second boss. I'll have a patch within like 10 minutes for that.