[Kunama]

I have the Markins ballhead on Manfrotto Carbon tripod which is excellent and would hold the camera at any angle I set it to, however, I have never liked hanging the camera gear off the side of the ballhead so I have the "Really Right Stuff L bracket" on my camera.

When I want to change from landscape to portrait mode, I release the clamp to the midpoint and reset the whole camera to vertical. This way the weight of my Nik D3/ AFS 80-200 F2.8 is always on the centreline of the tripod/head combo.

As for the the ballheads going past 90º, almost everyone I have ever owned including my Arca-Swiss go slightly past 90º to allow you to get it level without fussing about with the tripod legs.
For architectural photography the ballhead stays in the bag in favour of a geared head. As for levelling the camera, I use a hotshoe mounted bubble level, that way I don't waste precious time worrying about setting tripod legs, especially on rough ground.