I feel like this subject is one of the most misunderstood by even some of the core power user base.  As a general rule of thumb, using the Material Painter really only becomes a problem when you are using it to change a material that is being controlled by the structural layer settings of a parametric object or when using it with Blend Colors with Materials toggled on.  All other material changes made using the spray can are carried through exactly the same as they would be if you were to change