Teams got penetration on the edge which forced him to do what Coaches refer to as "riding the hump". Safeties are taught to get position and force the ball carrier to run backward as they try to get the angle on the hole the S took away. The stretch play in a zone read scheme requires the lineman to get down field at an angle.
That won't work when the O line allows the OLB or SS to set the edge that deep in the backfield.
The zone read scheme negates Mc Fadden's explosive burst that Lynch does not possess so I find the comparison 100% moot.
You nailed the issue which is penetration.