For me this is a huge issue, and one that I've sought advice on before. Rather than use the 'patch' tool, I've created modules, which have the virtue of being 'layer responsive', and can be updated globally as required. But the shear effort of doing this in order to resolve junctions which are clearly not right makes me question whether this is an efficient way to create working drawings - which have to be 'right'. Contractors would laugh at cavities which are bridged, or discontinuous when they shouldn't be, because that's the way the computer drew them.
Like Mauhaus, I've been very careful about wall priorities, but there are simply some junctions - particularly where 3 different wall types meet at a 'T' - where there seems to be no alternative to creating a patch. The attached shows an example where, because of the way the outer skin of brick masters the returned cladding, it would never be possible to achieve the detail 'automatically'. Notice that I've lost the skin separation in one of the composites, even though the make-up of these 2 skins is identical in each of the wall types (one was made from the other) and I'll also have to go back at some point and correct the fills at the internal angle.
If there were a better way to do this, I could find a hundred more productive ways to spend my time.