As of issue #14
As Flatpak is not a full Package-manager and not an Official one many Packages are unofficial or single Person maintained, it would be better to use the Distro Package manager. Let me give an example, especially in Enterprise environments if you have support from Ubuntu/RHEL/Suse often you only get support if you use a Package from their official Repository. Also taking Flatpaks or Appimage may be a high Risk in terms of Security, because there is no review/QA/Testing from the Distributions, thats why "use at your own Risk" is there a particular reason not to use apt/apt-get/aptitude on Deb-based and Yum/DNF on RH based Systems?
kind regards
Mike