From what I've heard, having not yet finished Divine Divinity, it sounds like it has three acts: Aleroth, Rivertown/Verdistis/Dark Wood, and the Wastelands. These are the only really linear points in the game. I imagine the Acts in Riftrunner will be story mile-stones.
Actually, they'll probably be different universes given that's what the game is about. <self head-tap> <img src="/ubbthreads/images/graemlins/ouch.gif" alt="" /> I wonder if you'll be able to rift back through the universes.