tl;dr; Flatpak currently considers remotes as trusted, so after you have
added one with a password at system level, you don't need a password to
install apps for that remote.

I don't about how polkit rules work, but this is just a comment
describing what happens from a user perspective with flatpak. If you
want to tighten it, I suggest discussing with upstream to ensure docs or
any other assumptions etc are correct (please also ensure any changes
make it into Debian, generally we have been able to avoid diffs with
Debian so far - we do have a diff right now as Debian is in freeze).

- Flatpak has two locations that you can add remotes and install apps to, user 
level and system level. System level ones are available to all users, user 
level ones are available to just that user
- Adding a flatpak remote or installing an app at *user* level does not require 
any password

So far I think this all makes sense, the interesting part up for debate
is the next part.

- When a remote is added to flatpak at *system* level, it asks for a password 
to verify the remote
- When an app is installed at *system* level for this trusted remote, it 
installs without needing a password (as stated in previous comments, assuming 
the user is in the wheel group)

To try this out you can do the following commands, the remote-add and
remote-delete will need a password, the install and uninstall won't.

$ flatpak remote-add --if-not-exists kdeapps --from 
https://distribute.kde.org/kdeapps.flatpakrepo
$ flatpak install kdeapps org.kde.kate
$ flatpak uninstall org.kde.kate
$ flatpak remote-delete kdeapps

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https://bugs.launchpad.net/bugs/1812456

Title:
  [MIR] libflatpak0

Status in flatpak package in Ubuntu:
  New

Bug description:
  Many applications have Flatpak integration using libflatpak. The
  Ubuntu desktop team would like libflatpak0 in main so we can easily
  build such applications. It takes a lot of work to make these
  dependencies optional and sometimes that is not possible. We don't
  need the Flatpak functionality to work by default and do not expect
  any other Flatpak packages to be installed by default.

  Default packages that have flatpak integration:
  - gnome-control-center (application panel).
  - malcontent (parental controls)

  Availability
  ============
  In Universe, builds for all architectures and in sync with Debian.

  Rationale
  =========
  Multiple default packages have libflatpak as a dependency, including 
malcontent (LP: #1892456).

  Security
  ========
  This will need a Security review.

  https://security-tracker.debian.org/tracker/source-package/flatpak

  There have been two CVEs, both have been fixed in all supported Ubuntu
  releases.

  More recently, there is LP: #1815528

  Quality Assurance
  =================
  Bug subscriber: should be Ubuntu Desktop Bugs

  https://bugs.launchpad.net/ubuntu/+source/flatpak
  https://bugs.debian.org/cgi-bin/pkgreport.cgi?src=flatpak
  https://github.com/flatpak/flatpak/issues

  tests are run as build tests (with dh_auto_test) and installed autopkgtests 
on Debian and Ubuntu.
  https://ci.debian.net/packages/f/flatpak
  http://autopkgtest.ubuntu.com/packages/f/flatpak

  UI Standards
  ============
  N/A

  Dependencies
  ============
  All in main except for libostree-1-1 (LP: #1892454)

  Standards Compliance
  ====================
  Package uses standards version 4.5.0.

  Maintenance
  ===========
  - Actively developed upstream
  https://github.com/flatpak/flatpak

  - Maintained in Debian by the pkg-utopia team but more specifically,
  it is maintained by Simon McVittie (smcv) who maintains Flatpak,
  ostree, xdg-dbus-proxy, xdg-desktop-portal and xdg-desktop-portal-gtk.

  short dh7 style rules, dh compat 10

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