As opposed to never using intermediary software: I always use Photo Mechanic to ingest files from a card reader to my hard disks. Using this process for the past 7 or 8 years, I have never had a problem, plus the software can accomplish several other tasks while ingesting, should I choose.
A card reader is faster and more reliable than using the camera. Plus not subject to your camera battery dying at just the wrong time. Card readers are not expensive.
You may be having good luck using the method you describe, but you are in a minority.