Going by the videos, they're all using the same guitars through the whole suite, and they're all playing Root in the same position you'd play it in Eb tuning.
Charlie and Rich from Haken both use Axe-FXs and I'm pretty sure you can digitally detune with it. It wouldn't surprise me if Eric did the same thing, but I'm not sure what his rig is. You can see him tuning during the intro to Root so maybe he just physically detuned it.
Connor(The bass player) is using an actual amp, so he had to detune his bass physically. Probably not the whole bass, you could get away with just tuning the E, A and D strings down and leaving the B, G, and C strings alone.
Boom, myth busted.