[aerohead]

Where the more-steeply falling roofline of the 'pup' is, technically, that steeper contour is going to create a flow deceleration and pressure increase, exceeding the 'threshold' for which the boundary-layer can remain attached.
It's the 'adverse pressure gradient' taught about in boundary-layer theory, always responsible for flow separation, which in turn is the reason for pressure drag, the main component of aerodynamic drag. To be avoided at all cost.
Lofting that contour back up to where the bedcover contour would continue, would reaccelerate the flow, restore a favorable pressure gradient, reattach the flow, and give you back, the otherwise lost pressure recovery, which will cut drag and rear lift, plus give you a little more useful storage volume.