Yes, this is common in database engines. Doing so allows you to optimize the file system along a very different set of performance tradeoffs and assumptions than a typical generic file system. Beyond that, it also gives you direct control of file system behavior, the lack of which is a source of code complexity and edge cases. This is not transparent to the database, something like PostgreSQL would need to have its storage layer redesigned to explicitly take advantage of the guarantees.

It isn't just about performance gains, which are substantial, it also greatly simplifies the design and code by eliminating edge cases, undesirable behaviors, and variability in behavior across different deployment environments.