... comparing stock to aftermarket head units in the same car, both with just the ear, and with empirical measurements makes other variables like dampening moot. ...
Subjective evaluations of audio equipment are notoriously bad. This is how we get "magic" silver cables costing hundreds of dollars being sold to the gullible. Most of the problem is confirmation bias (
https://en.wikipedia.org/wiki/Confirmation_bias), a very natural thing that we are all prone to. I don't want to get into a big argument here, but bench data is really the only way to know what you have. I say this from the perspective of working my way though undergraduate and graduate school as a broadcast and recording engineer. The empirical data in the Crutchfield pieces is interesting, though. I knew that car audio had to be bad, but I didn't realize how bad!
Most factory head units also have THD >10%, which is nothing to scoff at. Compare that to aftermarket head units which are usually <1% THD, you're definitely going to be able to hear a difference in SQ.
THD is a number that is meaninglesss unless a power level stated. Typically, it is quoted at the rated power of the amplifier. At lower powers is can be almost nonexistent and attempting to overdrive the final output stage will cause it to skyrocket. This creates a kind of dilemma for manufacturers who are selling watts. Claiming a higher wattage level necessarily means (if they are honest) reporting a higher THD as well. But of course this is not an industry that has been known for its honesty. I'd bet that at equivalent power levels and below any clipping level, THD for any car amp, OEM or aftermarket, and measured on the bench is going to be negligible.
I don't really have a dog in this fight, as I find the sound in cars to be so execrable that discussing aspects of its quality to be a waste of time. Whatever you like is best for you. That's pretty much the end of the story. What I like is my Klipsch Fortes and Klipsch La Scalas, conservatively driven and properly placed in rooms where background noise is not an issue. Those produce a quality of sound that is simply not achievable in a small tin box, even if the box is sitting quietly in a driveway.