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bbfa235
(Get the code!)
You're right. I can confirm that the runtime related refs are now installed without any issue, however the new code seems to have problems with downgrades. :-( Unfortunately, I am not a good in C so I cannot fix it myself and Joaquim Rocha doesn't work on GNOME Software anymore.
Other possible solution to the related refs issue is to switch to the new GNOME Software 3.30.* version in Bionic instead of using an older one. This solution is recommended by GS devs because the new GS has many fixes (not only the Flatpak ones).