It sounds to me like they may have grounded it to the chassis. Just need to find out where. Opinions vary in regards to where to ground an amp. I always grounded mine to the battery but I know some who experienced a whine so they needed to install an isolator between the alternator and battery to eliminate it. I do agree with your analysis that a sub and amp were probably installed.
2014 V6 Convertible Ruby Red Tint, Borla S-Types