I've not really looked into this but I certainly have had a roman and non-roman faction in BI 1.6 (modfolder) with the superfaction line under both entries in DS without any problems (except all that darn senate stuff popping up).

The senate stuff appears (and the block on attacking an ally) with the roman factions but not with the non-roman faction.

My own interest lay simply in a way to stop the Rohirrim and Gondorians from attacking each other (at least early on in the game).

Some factions seem naturally not to expand (or do so very very weakly) - can you not so set one up to so act or even block them off on the map of you have to - depends on what you are really trying to achieve I guess.

EB have elminated the senate I beleive and internally assigned the SABA faction to that tag - they may be able to help.