well, you are kind of looking at it from the wrong way.
nkpatcher runs off the hard drive, similar to an app, but is designed to be automatically launched upon bootup.
it patches the kernel in memory, so the original MS bios/kernel is not permanently patched, when powering off these patches are lost, and then the kernel is re-patched upon bootup.
restoring the hard drive to stock will remove nkpatcher, and prevent kernel patching, if you want to look at it like that.