What I am understanding from the atomics are that your view is right with caveats. Flatpaks only write to /home. But not all apps or software are flatpak. There is no standard for where apps write in Linux so some apps get wrote to system, some apps write to /home. Which allows creep and data scatter throughout a system.

It seems with traditional systems you gain good backups that are easy to redeploy should you need them. But config drift can creep up, updates break more easily, and rollbacks require up to date snapshots.

Atomics make rollbacks easier, but backups harder and more complex during restorations due to fragmented backup locations for different types of files. Also apps don't always play well with say SElinux on fedora but it's rare take Mullvad for instance its not a flatpak and they primarily update as. Deb or similar. Requiring distrobox or toolbox. Which is a whole other level of complexity.

I am basically trying to discern if I should go immutable or traditional OS install. Things sound great on paper. But daily driving is a different story.

I want security by default, sandbox/containerized apps, Wayland native, with solid backup support infrastructure. So not if but when and I do it often testing backups or re-deploying a machine. I can boot back in as close to never left as I can.

So continuity is paramount. I been eyeing fedora kiniote, fedora workstation KDE, Debian likely KDE. Only because cinnamon isn't Wayland native yet and likely won't be for a while.

Edit: Currently I been running NIXos. It's been great but config only backups up system apps and not data or app state. However even under /home backups you'll still lose system files unless their manually tracked and synced as well. It's one giant hassle. I used to clonezilla but my search for other DEs and OSes that scratched the itch for stock Mints flaws has still evaded me.