I'm not convinced packages need to care. Most config users care about on a SteamDeck is going to be Steam or game specific, so Valve are in a good position to put that on some mutable partition.

For the system data, which could be immutable, they could either take an A/B approach with two different partitions, or perhaps use either btrfs or ZFS to allow the new version to be applied over the old version as a 'diff' of the system partition. On a failed update, or to rollback for any other reason the system partition would simply be rolled back to the last snapshot.