I don't think Carmack ever worked for Apple. The XQuartz release notes say Carmack ported XFree86 (X server for x86 machines) to OS X; my guess would be that he did a limited port to get what he needed to run the Doom/Quake engine?
XFree86 wasn't x86 only, but the name does hint at how it did target PCs starting in a time when the norm for X would have been to run commercial Unix on non-PC hardware.