I was looking back at your earlier photos and got an idea, see if this makes any sense.
In the photo of the mpu board with the smaller piggy-back board, the eprom on that piggy-back board is labelled "PIXEL" and the other game software sockets on the board are empty. And U83 is missing. Or what I think is U83, I can't see the chip designator on the board in your photo so I don't know if it is called U83 (see photo below). What is your mpu board part number? I may be using the wrong schematic for a different mpu than what you have, if so, the following may not apply:
On some CalOmega mpu boards U83 is the cmos memory control logic chip. I think someone converted this mpu board to run the Pixel game on the smaller piggy-back board and they didn't want to save anything in cmos memory, so they removed U83 (or whatever that chip is called that is missing). They installed a socket in place of the missing chip, in case they ever wanted to go back to a different game that needed the cmos memory to work. But it looks like, for the Pixel game, the cmos memory feature is not implemented. The 6116 does get normal 5v power on the piggy-back board when the machine is turned on, so it can work as scratchpad ram for the 6502 processor. But it doesn't save any data when power is switched off.
I don't know what the Pixel game is, when you play the game is it important to be able to save high scores? Maybe it doesn't do that, starts fresh each time machine is powered up. The CalOmega machines were made for casino use, they required cmos memory to save certain financial data required by casinos. But if the Pixel game was for non-casino use maybe they didn't want the cmos memory to keep any info when the machine was switched off. That could be why you aren't finding battery power getting to the 6116 memory on the smaller piggy-back board, they decided it isn't needed for the Pixel game.
The other piggy-back board you have is larger, does it save the Pixel game scores when power is turned off? If so it is made differently and does bring the battery voltage to the 6116 cmos ram chip.
This is just an idea, let me know your thinking about this. And could you post a photo of the Pixel machine, I've not seen one before? Thanks!