I don’t know what to tell you @agingskier; I’ve always dumbly followed the instructions on this page:
sudo apt install flatpak
flatpak remote-add --if-not-exists flathub https://dl.flathub.org/repo/flathub.flatpakrepo
reboot
I’ve never installed “gnome-software-plugin-flatpak”, and I don’t use a graphical interface — neither “easyflatpak” nor even Bazaar (no more than “Software”) — I prefer using the terminal: at least you can see what’s happening.
After that, but only after that, I install Flatpak applications by copy-pasting the “Manual Install” code from the “Install” button:
flatpak install flathub org.keepassxc.KeePassXC
And I had never looked at $XDG_DATA_DIRS before you mentioned it.
Personally, I’ve never had any issues.
A couple of friends couldn’t access certain directories, but that was with very specific applications — hence my first recommendation to install Flatseal. 