The answer is easy.
Script based content, like pipes, would deployed as surface - not as volume model.
So you cant intersect a wall (3D volume) with a pipe (script, surface).
Its important to get piping parts as surface to keep the drawing size low.
I know a lot of cases where users build most parts of their piping material with 3d volumes in the catalog editor and let the sizes of their drawings grow.
BUT: There is a way how you could produce a improved visual experience with intersections:
1. export your drawings with "EXPORTTOAUTOCAD" into a simple Autocad File
- your piping material will change to 3d volume models after this step
2. copy all pipes who intersect walls at the same place
3. intersect the wall via substraction
4. create a ortho block via "FLATSHOT"
Otherwise: stay in your intelligent model and substract the intersections maually
Its a way .. but not the PLANT3D Way to create "intelligent" Arrangement.
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...you don't have to say please