Hi Willian Ely,
You ask "Neither the K60N512 or K60D100 boards have it so I thought maybe it was there because the K60F120 is a 120 MHz part (FSL put this on there for a reason, I'm just not sure what the reason is)." This is because the clocking system is not same, the main difference is K60F120 have a system oscillator1, and the K60N512 or K60D100 don't have it , so in K60N512 or K60D100 board ,there is no 12MHz.
Now I post the two chip's clocking diagram, it will make you understand more easier!
K60F120 clocking diagram:

K60D100 clocking diagram:

Of course you can cut down the 12MHz crystal, but make sure in your configuration don't use the system oscillator1
I wish it helps you!
Best regards!
Jing