But the os can't uninstall the native app at any time unprompted right

Corner case: actually, it can. Also, thats how auto-updating works ; depending on local state as a source of truth using browser apis is a terrible idea IMO.

The whole concept of "assume it is committed while we sync in the background" is, in the most cases, a terrible architectural decision, unless it is coupled with explicit feedback (eg. A small visual indicator indicating if the background queue is empty or syncing). Also, it breaks temporality: last-update-wins no longer holds, because update time and sync time are decoupled. And you also create a new problem, which is local cache coherence.

It may be a good fit for some systems (though I cannot think of a single one), but in general is just a horrible solution.

No, it’s definitely a lot less likely and probably an edge case you can ignore in practice