Reasonably sure that what you'll find is that the difference you hear between the USB and Hard Drive is the actual quality of the connection of the USB to the head unit... as more often than not, that connection ends out being a compromised Analog connection, rather than the Digital one that you would expect... typically the Car Head units offer Analog Inputs only and not Digital ones.

Using OBD equipment thru the OBD II port on all modern cars, you can usually (eventually) see what's on the hard drive (actually Flash memory these days) of a car. These "drives" are typically quite small and also need to have space for the usual 2Gb of Map data that it takes to cover Europe or the US... plus all the data that drives the usually comprehensive Touchscreen and all of the typical myriad options.

As a result, any time I've tested, the CD's have been ripped to the 'drive' as MP3 files and not WAV or FLAC as most of the Head units in cars are incompatible with those files.

To my knowledge, Mercedes are the only one who keep all of their connections (aside from the Headphone jack connection obviously) Digital all the way i.e their iPod and USB connections are Digital to the Head unit... and the Head unit is connected via Optical Fibre to the DAC & Amps in the rear of the car.

Down thru the years, I've found the iPod and USB connections available in most cars to be compromised in some way... even though the Dension iPod connection offered in some BMW's can also be quite good.

Summary:
The quality of the connections from the Inputs to the "Head" unit needs just as much 'tlc' as a home system... and car manufacturers either don't know enough, or care enough to spend the time necessary on the tlc

It must be remember that the Wiring Harness of a car is something that is developed and tested in Prototypes and Test Mules, sometime several years before the Final Model is produced... and it's only after all that test work has been done that people like Meridian, B&O etc. are asked to get involved... at which stage, it's too late to change the core wiring harness

As stated earlier, it's been my experience that Meridian, B&O, Harmon Kardon etc., should be considered as a "Layer" over the standard Hardware and Cabling that already exists in the base car. They are never given the opportunity (due to Health & Safety, Crash Testing and similar considerations) to change those "core" elements of a car audio system

None of this means that the Audio produced isn't "impressive"... nor that these Systems aren't an improvement over the standard systems (they mostly are... and Meridian likely more so)... and despite the sometimes compromised file compatibility and connections, these systems can add value, especially those who drive long commutes or journeys

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