By following KJSKOOG's suggestion and taking it a step further I was able to get the cleanup I needed (picture attached). Nevertheless, while it worked (somehow) I am still not clear how these layer priorities work:
First of all, you guys seem to be using the layer types quite liberally and seem to be only interested in the priority, and not in the layer type (substrate, finish, ...); e.g. the roof rock wool layer definitelly fits better as a thermal/air layer (from a type/function POV), yet you have no problem setting it as "Finish".
Second of all I got this condition by setting
- the roof rock wool layer to finish [4]
- the wall exterior final layer to finish [4]
- the wall interior final layer to finish [5]
So then it is clear that the roof rock wool layer [4] will cut through the wall interior final layer [5] (because it has higher prio)
But it is not clear why now it will not cut through the final exterior layer of the wall, since they have the same priority. How does Revit decide which has precedence? The "Switch join order" tool seems to do nothing here to change the way that the same prio layers cut each other (I think that would be the purpose of this tool). The wall and roof seem to be anyway not joined (becuse the roof does not get selected when I choose "Select Joined Elements" from the wall context menu), and using the Join Geometry tool on them has also no effect (no change in the "Select Joined Elements" result)