As listed in the test setup, they used TV sets (although really expensive ones) for the (U)HD setups. The Pioneer PDP-5000EX for instance has Pure Drive 2 software on it that I am not sure you can even disable. The software has MPEG noise reduction... It should at least be listed in the paper how to reproduce their setup, if they fiddled with the TV's settings.

I don't see any mention of how motion compensation and other "smart" features of the display devices influenced the perceived quality. Software in these devices may work in both positive and negative ways.