[greglepore]

Personally, I think that's overkill - so long as you don't terminate the 12v wiring inside the j box. All of the dc wiring should run thru the box to the xformer in its original sheathed cable, and the sheathing doesn't get removed until its clear of the 120v stuff. Your conduit to the lights likely terminates in the existing j box, so to completely separate out the wiring you'd need to put s bends in the conduit to relocate its termination.
Having the sheathed cable pass thru the existing box to an external location for the xformer is safe enough for me. This assume appropriate gfci and pool bonding, which is necessary regardless.
Not a pro, but I've done a fair amount of pool and spa maint...