Because SQLite isn't meant as a general purpose filesystem. It can do some things better (like, apparently, small blob storage), but not everything.
For example SQLlite vacuuming to free up deleted data can be slow, on large SQLite databases, we've found it much faster to rewrite the entire file than to vacuum it.
It also has some scalability limits, it uses locking to limit to a single concurrent writer (short duration locks), which only scales up to a point.
There're a lot of file system characteristics that differ from a database file format, SQLite could probably be more file-system like,but then it would diverge from being a fast and lightweight database format.
For example SQLlite vacuuming to free up deleted data can be slow, on large SQLite databases, we've found it much faster to rewrite the entire file than to vacuum it.
It also has some scalability limits, it uses locking to limit to a single concurrent writer (short duration locks), which only scales up to a point.
There're a lot of file system characteristics that differ from a database file format, SQLite could probably be more file-system like,but then it would diverge from being a fast and lightweight database format.
Microsoft tried the database as a filesystem once: https://en.wikipedia.org/wiki/WinFS (though this goes beyond just being a container)