I didn't look what that python script does, and I'm not sure what you mean by "point data". But if you export the sidescan mosaic to mdlayer or whatever it's called, you can import that into QGIS as a georeferenced raster. In QGIS there are functions to extract points from rasters, so that you could get the amplitude of an echo at a location as a point that is georeferenced. This could then be exported as a CSV. Actually, you could probably export to CSV straight from the raster too, or at least an ASCII format.
That is what I would do, if I understood correctly what you aim at getting, but then again I just recently started using ReefMaster so maybe there is an easier way of getting it from within the ReefMaster software?