That's a good question. I thought that was the case but I just double checked and it looks like you can load a VFS as an extension [1].

[1] https://www.sqlite.org/loadext.html

I can confirm that it does. I am working on it as I write this :).

Technically, an extension and VFS are separate things.

An extension when loads, allows you to register the VFS with the Sqlite. It can also register virtual tables as well.