Ok so the issue is actually one with Polkit not having policy set for non-local 
sessions, which this particular situation was. I was connecting from NoMachine 
(kind of like VNC) which uses ssh for authentication, so polkit was treating 
the same as trying to run flatpak from ssh. My "solution" was to append 
/var/lib/polkit-1/localauthority/10-vendor.d/org.freedesktop.Flatpak.pkla with:
ResultAny=yes

This allows non-local sessions to follow the rule set

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https://bugs.launchpad.net/bugs/1847339

Title:
  Polkit asking for password repeatedly when installing

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