Exactly what did your dealer find out?
RES can have the CD changer in its stock location, under the passenger seat. That leaves the driver's seat to house the subwoofer--which is convenient, as that's where Honda designed it to fit.
The NAV models have the NAV hardware under the passenger seat; this leaves only the driver's seat available, and you can put either the CD changer OR the subwoofer down there, but not both.
But there's no problem putting the CD changer into the RES model. And if you'll notice, the RES head unit is marked for the CD changer....
So exactly what did your dealer find out?