Noise level often depends on resonance of the roof structure and your factory A/C vent opening might be better reinforced than some of the vent cutouts. My 29 foot Winnebago has five vent cutouts, mounts the A/C over the kitchen (almost central and closest vent to power supply).
The A/C is not very noisy where it is located, much noisier 10-15 feet away, particularly in the over-cab area. So I don't think you can make assumptions about the living area being quieter if you move the A/C five or ten feet.
Should you decide to move it, you have to work out the wiring, how you might extend (or shorten) it and reroute it within the roof.