The video that people are criticizing isn't the first documentation of the allegedly different panels. Another fairly reputable site, AndroidGuys documented this issue much earlier, although it seemed to not receive the same amount of coverage:
The Tale of EVO Screen Woes: A First-Hand Account (With Video) | AndroidGuys
This kind of corroboration, along with the XDA information that there are two kinds of panels, Epson and Novatel lead me to reasonably conclude that there is accuracy to the suggestion that there are two panels, and that they significantly differ in contrast/color saturation/white balance... quality?
I'd also point out that in the video referenced, the reviewer does point out that the screen transitions when using the backlight control on the google powercontrol widget are very different between the two models. This isn't a "variation in output" or "screen burn in" issue. They are definitely two different panel designs.
The jury is out in terms of objective quality, but I would say subjectively, if people prefer warmer white balances and more color saturation (I think people generally do), then one screen design is subjectively of higher quality.