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I'm by no means an expert in this kind of processing however, looking at the 'before' and 'after' images, you can see how the really, really faint stars emerge when the background is subtracted .. which would mean that the process doesn't introduce too much more noise … which might then lead to artifacts appearing in the final image.
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Here is some science. Equalizing the data so that the Carina Dwarf galaxy had similar stellar densities in both images and measuring the sky background characteristics produced some interesting results.
Carinadwarf.jpg: Sky brightness:- 5574 ADUs, Noise:- 1612 ADUs
Carinadwarfprocess.jpg: Sky Brightness:- 34 ADUs, Noise:- 4 ADUs.
Not surprising that the Carina Dwarf was lost in the skyglow for the unprocessed image.
Regards
Steven