The filesystem defines how things are organized on the disk vs. the Operating System which reads/writes to the filesystem. The filesystem is a "layer" of the Operating System.
Think of it kinda like:
> A library can organize books by different methods, e.g. the Dewey decimal system or alphabetically by title. The librarian is the interface to the library and responsible for filing the books
> People (at the "operating system" level) only need to know how to talk to the librarian (the file system interface) to get or return books. People need not care how the books are being stored
Defrag and chkdsk are "workers" or "tools" that help maintain organization or fix filing errors that may occur time-to-time (e.g. cause if a library once held one million books and now only holds 1,000, it's much simpler if all those 1,000 books are stored close to together. Being close together makes it easier and quicker for the librarian to get them vs. having to get them when they're scattered across a large space)