To make GNOME Software 41+ stop autoselecting flatpaks instead of RPMs
Open a Terminal and check if option is available:
# gsettings get org.gnome.software packaging-format-preference
If above command returns No such key "packaging-format-preference"
you don't have the new GNOME Software version.
Set GNOME Software to prefer packages over flatpaks.
# gsettings set org.gnome.software packaging-format-preference "['RPM', 'flatpak']"
Re-open GNOME Software, the source selection will now always pre-select native packages.