while going through the reference designs, I came across the capacitor between grounds. Is it for RF noise protection? Is ground for U4 and other part of the circuit is different?
Its a NL\switchable part that is used for identification only (almost definitely). It appears that they use a capacitor to indicate what kind of board it is visually. On other boards, if the grounds were different on either side I'd say it was a ground connection but the ground is the same so it serves no purpose electrically.