It's loaded into the kernel, but it's a kext (kernel extension) rather than being part of the xnu source tree itself. Only a subset of kexts are open source. (By comparison, HFS used to be in the xnu tree, but it was moved into a kext as well a few years back; that one is open source.)

Kind of talking out of my ass, but Darwin can act as a mirokernel, so APFS could be implemented as a user mode service (no idea if it's the case, though).

Darwin's XNU is not a microkernel, in spite of there being a microkernel version of XNU. While Darwin does support FUSE, performance would almost certainly be inadequate, given the constant transitions between user and kernel space.

I thought it was a mixture of OSFMK and BSD, which is why I said it can act like a microkernel. Don't know more than what wikipedia says, though.

Yes, it is, but the Mach layer and BSD layer were fused into a monolithic kernel before NeXT Step turned into OS X. In OS X, HFS (and presumably APFS) are in the BSD layer.