The reduced data at CADC are mainly for inspection of the results, and also have not always been reduced with the latest version of the software.
They are reduced with the default DR recipe in the MSB, and for SCUBA-2 the default FCF was applied, which may not be the best for your observation. Also observations of different nights are not co-added.
You probably want to rereduce SCUBA-2 data using the correct FCF, the pixelsize of your choice, and possibly using external masks and other refinements.
For heterodyne observations the resulting files are often acceptable, but in some cases you may e.g. want to blank parts of the raw data or modify the velocity range with noisy pixels at the edges of the bands and rereduce.