The same behavior happens with plane cut. All of the the points were left as-is to preserve point IDs: Dynamic modeler plane cut type affecting number of points in output models - #3 by lassoan
Closed PR here: BUG: Remove unused points during plane cut by Sunderlandkyl · Pull Request #60 · Slicer/SlicerSurfaceToolbox · GitHub
We decided to leave the behavior as it was, but if it proves to be a problem then we can update it or add a flag to the relevant tools to clean the output.