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I prefer distro packages that are tied into the rest of the distribution and maintained in that context. That gives me a more smooth experience and some security because I know who prepares the updates and has a second pair of eyes on things. I like the sandboxing though. I think that should be implemented as standard for Linux desktop applications.
It's very hard for a project to maintain packages for all native packaging formats, though, especially for smaller projects. A universal packaging format is sorely needed and flatpak is the best we have right now.
One of the arguments for Snaps used to be that they are available on the sever as well. So one format supports server and desktop apps. Is that true for Flat packs? I honestly don't know.
Yes, there are plenty of server apps that are available as flatpak.
Oh cool that's good to know.