I'll try to answer your questions in order. And if anyone spots an error I've made please chime in.
It looks like the HEI ignition module, coil and spark plug are being used to generate a high voltage pulse to help start the plasma.
HF (high frequency) isn't necessarily bad for cnc but RF (radio frequency) will screw up communications in a hurry. Especially since this is using a spark plug outside of an engine block. It is basically a spark gap transmitter. This thing will have to be in a grounded box and all the cnc components and wiring will have to be grounded also to minimized the problems associated with RF.
What I read on that note about the relay was to disable turning OFF the HF start circuit. Meaning that it would be sparking all the time during operation.
The pilot start circuit adds a high frequency high voltage spark to the torch to initiate generation of a plasma at the tip of the torch. I'm only familiar with one plasma cutter torch but I believe that most (if not all) generate the plasma in basically the same way at the tip. What will be more important will be power handling of the torch you're going to try with this.
This is the first plan I've seen for a plasma cutter but you might check out some of the welding forums to see if anyone has made one. Here is one:
Was there any more information posted about this plan that might help explain things?
Good luck and let us know if it works out.