Yes we have to take the word of the slippery CIA that all was in order at the scene of the crash.
Yet it's odd how an F4 Phantom can disintegrate against a concrete wall like that video shown previously but an fully laden Airliner make all that damage and the heaviest parts, two 6-ton titanium steel alloy engines and not punch any holes in the outside walls while the tubular fuselage and soft bodied passengers and crew could penetrate so deeply into the building... and then disappear somehow inside in the flames...
The CIA and the FAA. I didn't see the video in question but what you describe really isn't that odd. The pentagon isn't concrete and an airliner isn't flying at near the speed of an F4. The engines may be the hardest part of an aircraft but even so, the center of mass is the fuselage.
As to whether there was any wreckage left at the Pentagon...Well really we have to take theie word on that as well don't we. It would be as easy to remove the wreckage secretly as it would to fake the crash. Just how far can we take a conspiracy? In either direction?