I believe every altitude/depth on that chart is given as the vertical distance above/below mean sea level. The depth of the grand canyon is not - the bottom of the canyon is around 1000ft above sea level, with the top of the rim at around 6500ft - on the chart it's shown at ~6000ft below sea level.
EDIT: It's so small... Unable to click... :(
would make more sense otherwise the canyon would be filled by water
I despise you