This is not really what I meant. I already was successful with creating the window holes with the Clipping Area.
I solved it differently. I used vertexes to define the vertical cuts and 3-4 different generators with Z offset and different Z size for the segments.
After that I just cloned and edited the base spline, lifted it and re-attached.
It was a very long process but since there were no pattern I could quickly repeat with Railclone so I just did it manually.