I don't like Snap packages. They are really slow at launching. Flatpaks seem more clean, run better and integrates better with the host system such as theming.
Really I've just never got around to giving it a try, but I've always just installed from the package manager & if it's not available then I've compiled it from source....
Flatpak is really good and easy to use. I use Fedora Silverblue so Flatpak is my preferred way of getting applications, otherwise I build an image and use Distrobox in order not to change the host system, which takes a bit more time. I'd say it's good for most things, except maybe the browser. Fedora's Firefox seems to be the most optimized and fastest one compared to the Flatpak version published by Mozilla. Also I avoid Flatpaks published by third-parties where security is important - for example crypto wallets.
i'm still confused about immutable. what happened when you need vpn or jellyfin/plex server stuff? do you just not use them? i know a lot of people just use vpn on router now, but unfortunately i can't do that with t-mobile wifi gateway.
you can install packages on main system - it's just best to avoid it when it's possible. I have VPN layered on the host system because I don't think thats possible through a container. Server applications can be run in a container and toolbox and distrobox make it easy because it makes the container applications run almost the same as on the host. With distrobox it's even possible to run an init system such as systemd inside a container. So I would say it like this: whenever possible, try to run applications inside a container or use Flatpaks. if it isn't possible then layer them on the host system.
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