Hi Markus
the geometry in your file is fine, and we are rewriting mesh intersections from the grounds up to make it more compatible with operations like the ones you need here. I want to make sure to mention that from what I can see and in our plans, all of these failures can be fixed, except maybe one, where you could maybe model the problem in an alternative way.
Because there are several robustness issues with the MeshBooleanUnion command, as well as with MeshSplit and MeshIntersect, in Rhino 6.
Regarding the modeling in alternative way, I’d suggest to modify intersections where flattish areas overlap, but do so only partially. This is particularly an issue on this side of the model:
In any case, right now, there is not yet a new version of the _MeshBooleanUnion command. It will come after MeshSplit will work more flawlessly. I have no solution to offer for now, I apologize.