Soooo, Ancestral Edition. Would that affect the Necromacer% run? Should it be something that has its own sub category?

Ancestral Edition includes Shieldbreaker and Crimson Court.

Nevermind, just booted up the game. You have the option to turn off all DLC for each save. Do I need to turn off all DLC? (Crimson, Districts, Flagellant, Shieldbreaker)

Yep. If you're doing Necromancer or Hag just uncheck all DLCs. If you're doing Courtyard uncheck all but Crimson Court