1) ShapeShifter disables the unified appearance because it isn't currently flexible enough for themers to use, and also because pre-Tiger themes would have looked horrible with unthemed unified windows. I'll be re-enabling it in a future version of ShapeShifter.

Disabling Unified even when default Aqua is the applied theme is a bug in ShapeShifter 2.1, fixed for the upcoming 2.1.1 release.

No clue on 2).