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.

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