It's very possible it all works as is, because you'll find some cabs have wired buttons 4 and 5 on the main connector, and only 6 off the kick harness.
Sure, and the Blast City is one of them. It has the 4th and 5th button on the jamma edge going to the 1P and 2P connectors in the CP. This is great for MVS, PGM and Atomiswave.
However, it's not great for Pandora. Pandora is Chamma. It has the 6th button where normally you have GND. It doesn't have a separate kick harness connector. So if you want to connect a Pandora to a normal, unmodified jamma harness, you need an adapter. Like this one:
https://www.mikesarcade.com/cgi-bin/store.pl?sku=JA-CHAMMA
The CHAMMA to JAMMA adapter moves the extra buttons to a proper CPS1 Kick harness plug on the adapter, allowing you to play the board in a standard JAMMA cabinet.
Can use a standard CPS1/SFII Kick harness for Player one and Two's button 4, 5 and 6.
If he gets that or something like it, he'll need a fully populated aux connector harness.
If there's an adapter that passes the 4th and 5th button through and only moves the 6th button to a kick harness connector, then yes, you're right, that'll work as is,
provided he has 1P and 2P harnesses with the needed 4th and 5th button wiring.
Also, the AUX connector is wired "wrong", so if he wants to connect button #6 for 1P and 2P, he'll need to use pin 3 and pin 5 on the CN8.
TL;DR: the current wiring is a mess and I would start over.