Move Windows shared/static options to later point

No need to do early and now is together with where those flags
are handled for Unix

Also warn if BUILD_SHARED_LIBS and GMX_PREFER_STATIC_LIBS don't
agree. And undo MD MT replacement if user changes
GMX_PREFER_STATIC_LIBS.

Change-Id: I66a165a7d3aebb31350bb13d19392d3f3935e54b
Merge "Move Windows shared/static options to later point" into release-4-6