Root directories are no go unless you specifically ask to change them. If you’re developing it’s a lot easier if you can depend on all the programs and dependencies to be the same in the same directories.

It’s like getting a system how you like it and burning it to dvd.

The changes from distro to distro are how they handle your changes. More specially how do we undo changes if it goes wrong

There are a few ways to handle changes some swap from image A to image B like vanilla os

Some just use their rollback image tech they have in standard distros like opensuse aeon .

Some like fedora silverblue use images that pull from a repo if you’ve used docker this might seem familiar.

From silverblue you have ublue project that really pushes the container ethos your distro becomes a host to ask sorts of containers kinda like proxmox.

The end of the day it’s like distros a collection a packages with the essential stuff locked in a non writeable directory.

I hope this is clear sorry I’m dyslexic and it’s bedtime