Setup/pedestal isn't stored on the disc (at least it's not supposed to be--Cowclops v2 might be an exception,) and it's not added to the digital SDI or HDMI outputs of an R1 player.
Since they're digital not analog, LFL's D1 or D2 master tapes shouldn't have setup/pedestal on them either. It would have been added while mastering the North American laserdics & tapes.
That said, I suppose the Japanese DVDs still might look better that their Region 1 counterparts for some other reason than setup.