OK I have a mk3 incoming and will test directly against the mk2.
Apparent changes are; the internal PCB's are redesigned, with the ground plane now on its own dedicated PCB with more of a focus on ground sink tech.
And the internal wiring is now Nordost mono filament. On the mk2 it was just normal stranded copper. If your incoming and outgoing power cables were all Nordost Mono filament solid core, running stranded copper in-between, even in short links, was always a compromise.
But I am a big fan of the QBase mkII after having used quite a few different power conditioners and parallel filters over the years. I thought it was just an empty box and too expensive, but it beat everything else I had and am glad I took the plunge to get one.
Maybe it has a special synergy with Nordost power cables and would not work as well with other brands, but who cares if you are on the Nordost train :/