Scan type could maybe have effect if it would be set to “Media store”. If it is custom it should not. But I had to check.
Getting tags back after missing images are back is due to the fact that tags are actually saved, and yes that is most likely due to Autosave.

As for your latest change in setting that seem to fix the issue. Normally, this should not happen. If there are default settings in “Included folders” and “Excluded folders” then there is no need to add any of those folders specifically.

Are you sure there is no “.nomedia” file in Downloads folder? If there isn’t, then I don’t see a reason for such behavior, and I would like to fix it. But for that you will need to contact me over email (support@fstopapp.com) so we can continue this investigation there.