When I was packaging Flatpaks, the greatest downside is
No built in package manager
There is a repo with shared dependencies, but it is very few. So needs to package all the dependencies… So, I personally am not interested in packaging for flatpak other than in very rare occasions… Nix and Guix are definitely better solutions (except the isolation aspect, which is not a feature, you need to do it manually), and one can use at many distros; Nix even on MacOS!
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