It’s not adding to the "Books" folder, but other random folders on the device, like "dictdata" or "koreader/data/dict/…". These get automatically checked.
So the actual process becomes:
- Connect device.
- Wait endlessly for Calibre to check all new unwanted folders.
- Go "Configure device" and untick all these folders.
- Restart Calibre, wait again.
- Desired result (only "Books" and "Download").