Model errors from npdet_to_step

### Environment: (where does this bug occur, have you tried other environments)
- Which branch (often `main` for latest released): main
- Which version (or `HEAD` for the most recent on git): HEAD
- Any specific OS or system where the issue occurs? No
- Any special versions of ROOT or Geant4? No

### Steps to reproduce: (give a step by step account of how to trigger the bug)
1. Convert the step file for PID subsystems
`npdet_to_step part -l 3 DIRC part -l 3 RICHEndcapN_Vol part -l 2 DRICH part -l 3 BeamPipe_assembly -o pid ${DETECTOR_PATH}/epic_craterlake_pid.xml`
2. View the step file with CAD tools (used OnShape website in this case)

### Expected Result: (what do you expect when you execute the steps above)
A correct model

### Actual Result: (what do you get when you execute the steps above)
Additional volumes that should not exist in the simulation model (see the picture below)
These additional pieces have the shape of the beamline hole.