Way ahead of you (regarding the walls being flush with the floor)! I actually made this suggestion back in the following thread a few months earlier (before multi-story mechanics were implemented):
Foundation Blocks to Erect Walls?
(Obviously, it’s a little out of date now with the current mechanics, but the basic argument for flush floors still stands.)
As for internal walls/doors/windows/etc., we’ve yet to see this mechanic in the GUI. You can get away with a little bit with the free voxel tool, but Radiant will be adding these as an actual feature in the future (think of it as Building, ver. 3).