If the CIA/FBI wanted to make people think a plane had hit the pentagon, why wouldn't they just use a plane? This conspiracy theory is one of the dumbest.
Gov confiscated all footage of incident is not the same thing as because incident nature was x and they were conducting a coverup.
(I have no idea if the footage was confiscated from all people, only that the footage from certain fixed nearby locations was confiscated, and have never seen any proof this was done because it was a coverup attempt.)