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For me the main con of Flatpak and similar systems is that it's complicated and messy. Why duplicate a lot of libraries unnecessarily? System packages all rest on a single integrated layer of libraries. It's simple (as in simplicity) and therefore unlikely to go wrong.
In my mind... I can use the system packages, and run with a more stable experience for the majority of things that don't *really* need the latest/greatest version to work just fine.
But for the occasional thing that either a) isn't in the main line repos, b) the version in the repos is *ancient*, and lacking features I want/need, or c) the version in the repos has a bug/glitch... flatpaks give me an easier alternative than some of the other options out there. But as mentioned before, they can be... untidy... at times.
I think flatpak and similar is an over complicated kluge, plus I suspect it may actually encourage maintainers to ease up on security. My thinking is, since it is cordoned off, no need for security.
I wish Linux would go all in with something like OpenBSD's pledge and unveil. These are easy to use and gets the developer thinking about security instead of having the program "in a box".
I know someone was looking at pledge/unveil on Linux, but due to how Linux is designed, getting it 100% like OpenBSD is quite difficult.
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