This is a usual flaw in this game's design/engine.
If a mastery is added by a DLC, bonuses to that mastery or its skills are mostly if not always added to items that drop in the new areas of that DLC. So items that boost Neidan are found only in Legendary, in the Neidan map. Maybe Electrum Orbs from "the East" can work too.
I think the main reason is the engine, it doesn't adapt the loot or the mastery/skill bonuses to the DLCs you have.
So instead of dropping Neidan items in all acts, and that would also be for people who don't own Eternal Embers, they make them drop only in the EE map. Or maybe Electrum orbs, but maybe those are locked for people who don't own EE (if so I don't know how it's done)
It was a bit of the same with Dream/act 4 (now that it's tied to the main game, a few Dream items have appeared outside of act 4)
And same for Runes/Ragnarok.
Edit : I think they added Neidan bonuses to stuff you find in the Hardcore dungeons (head armor from Immortal Hero or Chaos set, Perseus' Discus). Also an Epic ring in Atlantis (Shine of Pandia) and a Legendary throwing weapon in Ragnarok (Chakram of the Sun). Those are kinda exceptional and found kinda late in the game.
