Just a bit higher in the manual (on the same page as your first picture) it shows where the +5 and +12 comes from for that 3 holed (GROUND, +5, +12) connection that the game originally had.

The +5v is from the J16 pin 7 and the +12 is from the J16 pin 3. So those are definitely safe to use if you want to get into them....as that is where the original "PRINTER SUB-ASSEMBLY" connection that many Whitestar and SAM mods used for power, come from. It doesn't specifically say where the GROUND wire is run from, but I would expect it may be from one of the 6 GND connections on the J16. I'm not sure why that wouldn't have been noted in the manual along with the others.

In all of my time of selling the Speaker Light Kits (since late 2012) I have never heard a report of a game not having that 3 holed connection that should have had it (Twister - The Walking Dead). I did hear a report of one acting up and the +12v wire only providing power sporadically due to a bad connection somewhere, but no one saying the connector was hacked off or removed. I was actually a bit concerned about that early on, as I had heard stories about re-import games having normally unused connectors hacked off for seemingly no reason.

3 holed +5v +12v (resized).jpg