Add...
[General]bAllowMultipleMasterLoads=1
... to SkyrimEditor.ini, then select the new master you want to add, tick it, set your plugin as active, load, save. That plugin should then be able to reference/override forms from both masters.
NOTE: Currently and unlike the engine, the CK will only allow ESM masters.
What about esmified ESP's? ESP files with the ESM flag switched in the plugin header? That worked in Oblivion.
That's the goal I think. A "mod" that is completely independent from the Skyrim.esm.
It appears at the moment that I'm going to have to go through and import all of the objects and basically start everything from scratch.
I have a cleaned Skyrim.esm of only 8 MB, all worldspaces and quests are deleted, but also all magic effects and anything related to magic and all perks are deleted. This is the base MERP will use. You can have that Skyrim.esm, but if you want magic you'll have to move all magic related forms back in using TesVsnip. I also had to remove some idle anim conditions because they referred to deleted forms, so if you die a greybeard anim will play. Should be easy to fix though, just got to add a new valid condition to those idle anims.
Anyway, I cleaned up Skyrim.esm with TesVsnip in 2 full days, it's an insanely boring tasks to remove all conflicts caused by missing forms that other forms refer to. But it's definitely possible.