> But the most obvious alternative to a filesystem would be formatting a whole hard drive as an sqlite database.

At the end of the day, you'll be chasing pointers inside that SQLite database, where you store tables, indexes and such. Interestingly, this is how a filesystem works. Tables, indexes, redirections and fields. Very much like a database. EXT4 is a table of redirections, nothing fancy [0].

[0]: https://blogs.oracle.com/linux/understanding-ext4-disk-layou...

Yes, believe it or not, all memory gets populated with data structures to be useful. That doesn't mean all data structures are equivalent.