Since you can set the distance for the speakers (including sub), the processor will impart a digital delay. For most applications, this will insert the phase delay you need to keep all the wavefronts aligned at the listening position.
Where it gets tricky is bypass, pure, or direct mode. If that truly bypasses all internal processing then the sub would be on its own for phase control. The only way to know for sure is to use measurement software and do some before and after with impulse or time-energy plots to see if the sub and mains are aligned.