How does part of a microprocessor (Apple secure enclave) use a microkernel (L4)?
The Secure Enclave is a separate CPU core within the CPU. It has its own RAM, ROM, etc, and consequently runs its own separate OS.

You can think of it as a computer within a computer, and that "inner" computer is heavily firewalled off from the "outer" computer so only certain data can pass from one to the other.

The theory is that your especially secure information (biometric ID data, etc) is only within the ultra-secure core and can't be accessed by anything else.