If it works with scanimage, it should in theory work with NAPS2. The fix is likely to be easy as long as you can find a relevant error message in the logs.
Also I should mention, if you're using a Flatpak that won't work with external SANE drivers and you'll need to install the DEB/RPM.
What exactly is the output from scanimage -L? Is the scanner listed? If not, it's an issue with SANE and not something that can be fixed on the NAPS2 end. If it is listed and not showing up in NAPS2, that's potentially a bug and you should check the error logs. The relevant code would be here.
It's based on the resolution of the JPEG images, which you should be able to change in most image editors. e.g. the bigger ones might be 72dpi (dots per inch) and the smaller ones might be 144dpi.
Both of those look like they have text to me. Sounds like an issue with your PDF viewer, Firefox/Chrome/Adobe all show it for me when I press Ctrl+A.
Do you have an example PDF you can attach?
Yes, in fact - next release, in a few weeks hopefully.
This should be fixed in 7.5.0.