Never going to happen, too easy to modify the custom faction for all kind of cheese. There's a reason the MP files are separate from SP files, that's to preserve fairness.

They should simply have the ability to have custom factions/sovereigns, and after the initial save to your hard drive is done, do like VAC does and check whether or not the files have been modified since initial creation. Of course, I have no idea how big a drain on resources this would be to Stardock, so for the moment, no custom factions/sovereigns is fair.

Everyone just play Ythril (: 

Anyway, custom sovs and custom factions won't be in for a longggg time.