Really dragging the brain cells out here but I thought it was because the ND ETA shows estimate based on current groundspeed whereas MCDU has wind factored in based on entered info.
As an e.g., going oceanic with 460+ nm between waypoints, when crossing each waypoint you needed to give the estimate to ATC based on the MCDU info as the ND would be out by a good amount if there was a wind change during the next leg.