Rear end howl

Ford is telling you this or is it the dealership tEcH or SiRvUs mAnAgR? There's no way Ford would ship a mainstream product expected to make noises like that. Ford's "Traction Lok" LSD is not known to make any such noises under normal conditions.

Having issues like this on an 07 with such few miles is very unusual. The first thing I'd do is source a new dealer. Second, I'd have them change the rear-end fluid ensuring they know to add a bottle of friction modifier to the new lube. If that doesn't cure the LSD noise then it'll probably have to come apart for forensic analysis...

If the rear has been unmolested it's possible that Ford's warranty would cover it, no? The dealer dolts may be telling you its normal to wriggle out of that responsibility. If they think its normal then don't allow them to service the car. Clearly they don't know enough about rear axles, hypoid gearsets, plate-type LSDs and so on to be wrenching on one...