I recently learned however that the SteamOS desktop is built on a read-only image, with the expectation software will be installed via flatpak.

It is apparently possible to turn the read-only protection off to use pacman or your own thing, but anything you do may be wiped out on the next OS update.

See: https://help.steampowered.com/en/faqs/view/671A-4453-E8D2-32...

I believe it was mentioned in a previous story that it would at least not void the warranty to replace SteamOS entirely though.