1. Yes, kinda. This apparently breaks your ability to easily switch back to game mode, but you can still get back there by running the second command below and rebooting.

to boot into desktop mode by default

steamos-session-select plasma-persistent

to boot into gaming mode by default (and to fix inability to go back to gaming mode from desktop)

steamos-session-select gamescope

2. It will last until each update. Updates happen via an A/B partition switch, so the other partition gets updated, then that one becomes the default for booting (both still technically boot, but the original image will be behind).

3. If you mean accidental changes by you, then it would be steamos-readonly enable. Note that changes happen via a persistent OverlayFS. Re-enabling might remove that overlay and your changes. Test with something easy to see if it persists. Note point 2 about permanence.

4. Don’t bother messing with the system files if possible. Try to use an AppImage or Flatpak instead, as they exist in userspace and will persist over updates. The issue is that it’s the core system files that are written to a new image each update, not your home directory. Your home directory and settings will persist.

If you want something modifiable but still atomic, Bazzite is a good option. You can apply rpm packages via layering, and you can install packages from other package managers via distrobox. You’ll still have the safety of images as restore points. If you want a more traditional Linux experience, though, look into something like CachyOS.