Most packages are purely additive to to system. If GNOME is part of the base system, I don’t care because I can just not use it. For packages that are mutually exclusive, well, usually that’s the distro picking it for you anyway, but if you insist on changing them then OverlayFS lets you mask files in the base.

For something like Arch or Gentoo, the read-only partition approach absolutely won’t work, but I know Fedora’s been working on an OSTree immutable approach, so it’s still technically a mutable partition but it’s defined declaratively and is still easy to roll back.