that the bathrooms should be stacked on top of each other (because wastewater is not beam transported away by Scotty), and that vent pipes "like" to go straight up.
I absolutely agree with you, it is definitely easier to solve that way. But a good architect can also fulfill such wishes. In our case, the bathrooms on the ground floor and upstairs are all offset against each other. Under the bathrooms upstairs, there are rooms on the ground floor, and above the bathroom on the ground floor, there is a room upstairs. In not a single room does a pipe run on the surface or is there a boxed-in ceiling, despite additional piping for a central vacuum system, etc. We also didn’t need any strange walls for that. All rooms are well laid out, and there are clear sightlines in the hallways. Together with the structural engineering and so on, it’s not easy, but that’s exactly why I commission an architect and not a butcher to solve it.
My impression is just that many architects are not really exerting themselves much for single-family homes. They prefer to build residential complexes, office buildings, etc., where lots of volume also brings a lot of fees. That is basically understandable, but it is not satisfying for the client.