If it isn't client / server architecture there's no privilege separation using SQLite either. The storage format isn't the concern. Rather, the concern is it all runs in the same OS security context.
Exactly, or an access database. This is to enable end users who live in a fully locked down environment (enterprise setup) and can't install anything to use database like features without having to wait 6 months for IT to lift a finger.
But if it starts being a system of records / authoritative system, there needs to be a plan to decommission it.