There is one major difference you are not taking into account. The vector of the forces involved is completely different in these two cases. In the Sandia demonstration, the force is directly into the wall; at the Pentagon, the force is at an oblique angle to the foundation. At the Pentagon, the force is directly into the outer wall, of course, and that certainly shows the damage we would expect. And of course, if the damage was caused by the sort of bomb you seem to think (judging from your "up and out" comment), there would most certainly be force directed down toward the foundation, and there would be more damage than your photograph shows. Look at any of the news photos of IEDs in Iraq, and you will see craters in roads, dirt, buildings, etc.
I think your photo demonstrates quite clearly that the forces involved are inconsistent with the sort of bomb you are proposing. They are, however, consistent with a crashing airplane.