There's a laundry list of benefits that all add up, not like one specific killer feature. Some applications really do have very complex configuration needs, but it's sorta situation dependent on whether embedding a scripting language or a database is the right solution (for really simple cases I'm more likely to reach for TOML).
An incomplete list of benefits of using SQLite:
- Runtime config changes for free
- type safety
- strong migration support
- incorrect configurations can be unrepresentable (or at least enforced with check constraints)
- interactable from text-based interfaces and strong off-the-shelf GUI support