Considering they're using a seperate update .esm, I'd say Dawnguard will have it's own .esm as well.
Yeah, makes sense. Moreover, there's going to be more expansions, which would create a total mess if they all had to be patched in.
Yes, it works the same as the Vampire Lord tree.
What bothers me about the vampire perk tree is that it seems to be locked to the special volkihar vampire type that you become in dawnguard. Maybe a skilled modder could retool it so it becomes useful for normal vampires as well...?