I don't recommend doing this. Pixel size is mainly for doubling or halving the sprite's logical dimensions. What you're doing is... well, kinda nitpicking.

-- and it won't give you nice results.
Fixed size is indeed the easiest setting to use when developing UIs. It will keep everything the same proportions. Using anchors to glue elements to the corners or sides of the screen will also eliminate the "extra space" you mentioned.
Nicki can give you better advice here than I, but I'd suggest creating two layouts -- one for iPhone, and another for the iPad, and only two atlases -- HD and UD. Since the sprites in the UD atlas would be twice the size of those in the HD atlas, the pixel size scale setting is trivial, and any inconsistencies between iPhone and iPad would be addressed in having the different layouts.