I've been playing the Wrath of the Necromancer and I noticed I've only been getting the new bosses.
Is that the default now or do the Vanilla bosses still have a chance to spawn in?

Based on my recent experience, yes the original bosses can still spawn. I started a new Wrath of the Necromancer game and while the DLC bosses populated the first 2 floors, I drew the Monster Hunter on the third floor. No idea what the chance is for one boss vs the other (I'd guess about a 50/50 chance), but it can happen.