I think SPHARM-PDM will only accept VTK file of models (with no gaps). For consistency between the models, and to make sure there is no gaps in the models, you can use data-importer module (in SlicerSALT). This module should be helpful for checking the models, before running SPHARM-PDM.
N.B.:
After trimming the condyle, the model will have a gap (that need to be covered before exporting to SlicerSALT). In 3D slicer, you need to cover the exposed-region of the models (so the model does not have any gap).