Maybe, some work which I did before can help you to make this change:
https://discourse.ubuntu.com/t/ideas-for-improving-the-experience-with-
flatpak-packages-in-ubuntu/39643/16?u=milachew

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Packages, which is subscribed to gnome-software in Ubuntu.
https://bugs.launchpad.net/bugs/2056767

Title:
  DRAFT [FFe] gnome-software package split

Status in gnome-software package in Ubuntu:
  Incomplete

Bug description:
  As requested by the Ubuntu Release Team, I am providing early notice
  of a Feature Freeze Exception I intend to request soon (later this
  week hopefully) to split the gnome-software package into separate
  binary plugins. This will allow users and flavors to specifically opt
  into the parts of the GNOME Software experience they want. For
  instance, someone may want to use only the Flatpak part or only the
  apt/.deb part.

  What is Needed Now
  -----
  Finish the Salsa merge request to get some review from others.
  Evaluate different use case workflows and how well the changes help and any 
issues that may result

  Impact
  ------

  Potential Problems
  -------

  
  Other Related Changes
  ---------------------
  fwupd

  
  Desktop Flavors Affected
  ------------------------
  GNOME Software is currently included in the default install for only
  Ubuntu Cinnamon

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