Part 1: There is an area of study that is the subjective responses of the human body to vibratory motion. Define it as opinion or science if you want. That's a separate debate. You essentially end up with a graph of vibration frequency vs. vibration amplitude. People tolerate more amplitude if the frequency is lower, and less amplitude as the frequency increases. There are several levels of response that vary from 'perceptbile' to 'disagreeable' to 'intolerable'.

It is entirely possible that the ride preferences due to frame design are small to the point of vanishing. I've ridden bikes that would make me question your hypothesis, but I'm willing to accept it as a starting point. If that is the case, then it is worth finding out. At that point a manufacturer knows they can build the frame any way they want to and worry about optimizing other aspects of the design while not having to sacrifice ride quality.

Part 2: Instrumenting a frame and testing a variety of tires and/or wheels would also be an interesting project, and completely worthwhile to a manufacturer IMO. So if that is a worth study, why is it such a stretch to leave the wheels/tires constant and swap frames?