What does OS 3.2 use natively?
It uses the default file system
The Amiga operating system has a designated "default file system" which is baked into the ROM. You can set up your hard disk/SSD/USB stick partitions to each use a different, specific file system such as PFS3 or SFS, but in the absence of you doing so, the responsibility for managing disk storage space will fall to the default file system.
If you list all the components by name which make up the Kickstart ROM contents you will find the default file system under "filesystem". This is the component which knows how to mount, read and write disks and partitions formatted using the FFS, DCFS, LNFS, etc. variations. A version of that "filesystem" component can be found on the installation disk under "L:FastFileSystem". It's basically the same thing as the "filesystem" in ROM, but can be used by HDToolbox to make partitions use that specific file system version.
What makes the default file system peculiar is that it has to support the complete documented feature set of what an Amiga file system could possibly do. This includes, for example, support for hard and soft links, file record locking, file/directory notification and even legacy API/data structure quirks which result from how dos.library expects the default file system to behave when the system starts up. This is why you cannot generally replace the default file system with a different one if you wanted to. The replacement would have to fill its shoes, which is a tall order (tall shoes, if you will).
