What I’d suggest is to do the whole workflow in Slicer. It can import the CBCT, and you can do nice visualizations of it. Segment Editor is probably the most advanced freely available manual and semi-automated tools out there, which can save the result to STL, DICOM SEG, etc. If the Intensity Segmentation tool you referred to is essential to your work, then as @lassoan said in this thread we can probably easily add it to Segment Editor as a new effect. You won’t even need to use Model Maker because Segment Editor takes care of the conversions internally.
This is how such a workflow looks in Slicer: https://slicer.readthedocs.io/en/latest/user_guide/data_loading_and_saving.html
Update: Making CLIs Segmentation enabled would solve this problem too. Then there would be no need to add an effect for each segmenter CLI.