Retired from the swimming pool industry and never made a transition from 120VAC lighting to 12vdc lighting but... Best practices with lighting, audio, and machinery always suggest physical separation of 120VAC and 12vdc circuits. I would not connect them in the same J-box but I would still have a bond wire from the underwater fixture connected to everything else (bond wire is different than green ground wire).
This is the current Florida Code for submerged luminaries and it appears that a bond or ground is not required. The J-box for 12vdc does require separation from 120VAC circuits. I hope this is helpful. Pentair tech support line also used to be very helpful when you hit a snag like this.
Cheers!
https://floridabuilding.org/fbc/thecode/2017_Code_Development/2017_Resources/Swimming%20Pool%20Electrical%20Safety%20-%20fact%20sheet%20-%202016-06-30.pdf