Thanks for investigating further, yes [0] seems to be the issue
upstream. I'll keep an eye on the pull request/issue and hopefully it
will land into a release that can be SRU'd :-)

0 - https://github.com/flatpak/flatpak/issues/25

** Changed in: flatpak (Ubuntu)
       Status: New => Confirmed

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https://bugs.launchpad.net/bugs/1801814

Title:
  Environment overwrites XDG_DATA_DIRS

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