Currently no, but I think this is a feature request that has come up before. I don’t know if we’re tracking it already on GitHub. If you find it, please link it to this thread? If there isn’t one, could you open a feature request on GitHub?
I think right after the georeferencing step, before the cropping calculation (odm_georeferencing.py:177). This would involve adding a PDAL call to crop the georeferenced point cloud given a polygon boundary.