Android userland is vastly different from ‘linux’ ie desktop linux people are used to. While there exists unshare/proot based containers (termux is an example) it might not be suitable for privileged features of kernel except for rooted devices.
Chromeos is much closer to desktop linux (init being upstart not systemd afaik) but still the ‘linux’ apps run inside crosvm to keep the locked down nature of the os intact.
It always worked for me except in some cases the ‘hardware’ compositor (ie the wayland side) is a bit buggy for clipboards and inputs in general. I had issues with lxc network in past but that’s long ago.
I still don’t understand what borked your system. Waydroid downloads the images, mounts and runs them inside lxc just like normal android. It doesn’t touch your /usr or anything else. Works well in immutable os too.