.. in my opinion, this is only a workaround, and sorry, I'm a perfectionist, and workarounds are only temporary solutions and for me not acceptable.

So, this is where I disagree. I do not see manually adding SVG for advanced models as a workaround. Quite the contrary. For models with complicated shapes, it will be better if SH3D does not make assumptions about how to cut / intersect with other surfaces. Letting the model maker (or the user) is - I think - much more professional, or perfectionist if you like.

After a long night of studying my possibilities with sh3d, FreeCAD and Inkscape I could not resist to give your solution a try, and now I have to say yes, you are right, this is a solution. It's absolutely not as much effort as I thought it is, but it's even not the simple solution sh3d should offer for most of the end-users.
Group Cutout
But as you can see in the picture, the groups still cut big holes. Is there a possibility to define groups do not cut anything?

BTW, the staircaseCutOutShape-entry for the hull is exact 66662 rows long...