Some Linux filesystems, notably ext4 and XFS, provide the necessary features to get 90% of the benefit simply by using O_DIRECT correctly. The last 10% is achieved by doing direct I/O to raw block devices, with the obvious caveat that this is not as easy to manage.

Both of these are commonly done in database storage engines.

If you preallocate and O_DIRECT, haven't you basically soaked up most of the benefit of skipping the filesystem?

Because the speed increase is - on modern, properly tuned filesystems - surprisingly small, due to how RDBMS's manage their pool; by working on large container files, they avoid most of the filesystem overhead.