That’s a good point. I’ve just installed Paperwork from the testing repositories, as you recommended. And I get a few steps further than with the flatpak. 
When opening the settings dialogue, Paperwork detects the scanner, the default source (“feeder (left-aligned)”) and sets the resolution (“300 (recommended)”). This didn’t work with the flatpak. 
However, when I start the calibration scan, the popup
Error while scanning: Error while scanning: libinsane-quark: Libinsane opt[mode]->set_value() error: 0x400000003, Invalid value (4)
appears again. This is the terminal output: https://andwil.de/temp/paperworkdiag-2020-07-05.txt
Can you find anything useful in there? The basic issue still seems to be the same. :-/