Well, just reverse the scenario. If you set up a JAMMA PCB to run from Nintendo-style wiring, would that somehow transform it into an original "Arcade" submission?
Of course not. It's just wiring.
All the JAMMA harness (or any other harness) does is control where electric current is going/not going.
The "JAMMA" category refers to the actual PCB you're playing from, not how your cabinet is wired.
I don't think this could be a debate even if someone wanted it to be!