Check out what the ME disable stuff does. It just removes some of the binaries from the thing's uKernel that are the non boot services. The ME is required for system bringup.
> However, while Intel ME can't be turned off completely, it is still possible to modify its firmware up to a point where Intel ME is active only during the boot process, effectively disabling it during the normal operation, which is what me_cleaner tries to accomplish.
https://github.com/corna/me_cleaner
EDIT: Also, the ME is inside the PCH, so I'm not really sure why you're making a distinction there.