The second design flaw is manufacturing stretched airplanes in the first place, which are hacks in general. Even as an amateur one can see that the proportions are off without understanding anything else. They look ugly and fly ugly.
The stretched cargo version of the MD-11 had many issues and accidents, particularly during landing.
While there is something to the notion that if it looks like it will fly it will fly, remember that the general configuration of modern airplane design took many, many years to settle down on. Even the Wrights got it wrong (putting the stabilizer in the front made it unstable).
The notion of swept wings, that seems so natural today, was a very long time in coming, for another example.
For a third, the aerospace people keep finding ways to make the wings more efficient. Notice the winglets on the wingtips? Those are fairly new.
The stretched cargo version of the MD-11 had many issues and accidents, particularly during landing.