You're absolutely 100% correct that ears are the only measurement tools that matter. The ears are the end goal, period.
But when you draw conclusions about something -- anything -- you often need to employ other tools so that you can identify what it is that you're concluding! If I listen to your car and then listen to my car, and hear that there's a huge difference, I can't conclude, "Well, there you have it! You and I used different speaker cables, so therefore our speaker cables provide vastly different sound!" That would be foolish. We would have to identify what component or what aspects of the environment are responsible for the differences we perceive -- can't just pick one of the many possibilities and go with it. So, for that example, I might electrically measure the individual components (or at least the speaker cables) to identify whether the speaker cables are in fact responsible for the differences observed.
Again, nobody is challenging your assertion that you hear a difference. The only challenge is that you identify the offending component. You might argue, "I only swapped out the head units and nothing else, and therefore it must be the head unit." But you haven't demonstrated that 1) the output settings were the same; 2) the operation was at a constant level (vol controls are different); 3) the tone controls/DSP were flat; 4) the units were operating within their linear ranges. That's where measurement tools come in.
And this is important, because it greatly alters the conclusion that one can draw.
You asked for credentials -- I don't have any credentials to provide regarding listening, aside from having played instruments for a little over 20 years. I do not work in the audio field, although I am an engineer who has performed these sorts of measurements in a professional capacity for about 10 years, and I have expertise in performing sensory testing for several years as well.
The OTs question: is there a difference between headunits? Of course there are! Can the differences with distinguishable to the ear? In most cases, I'd say no. There's audible sound degradation among noise and crosstalk parameters (on some cheaper units), other than that I find it highly unlikely to hear differences. If there's no difference, why the hell did I buy a Pioneer P99RS then?!? Because it has an awesome built-in DSP with 4-way capabilities with a 31b GEQ I can change the sound however I want to. It got awesome iPod control, nice display, good build quality and some other really nice features not available in cheaper models. Just saying, buying highend models gives you features to make the unit sound however you want it to sound! If you have the money, why hesitate. If you don't have the money, spend it on other things like installation where the real difference can be found.
I rephrase the question: Head unit upgrade = better SQ output = YES, if it does have a DSP built in. Definitely, it's absolutely necessary imo!!