I hope. In Morrowind, we had three great houses. You could only join one because the tensions were too great. While that may sound bad, it was actually a really great feature. No one character could play through all factions.
But I don't believe they could give thieves an upper hand by letting them join two factions :shrug:.
Unfortunitally, I believe he meant tensions between minor factions and the Companions/the college. Such as Necromancers vs mages in Oblivion. Or fighters vs blackwater.