Eh...don't really see where you disagree with Chomsky. He just rebuked the claim that the orchestrated it.
Complete negligence due to complete hubris and collective narcissism is about accurate. The entire neocon mindset is pure arrogance and megalomania. Motherfukkers really felt they had the military and economic might to take over the whole world, and the divine right-like moral justification to do so. They spell it out in the PNAC literature. There were warnings: the infamous PDB about Bin Laden being determined to strike, the reports from Richard Clarke's counterterrorism team. There's nothing to suggest that they knew that specific attack on that specific day in the manner in which it happened.
Those arrogant dikkheads just felt they couldn't get touched by some inferior Arab savages in their mind.
They didn't learn lesson from their arrogance either because they thought they could take over Iraq with a few hundred thousand troops and some establishment bueaucrat cronies including well-connected grad students, none of whom spoke Iraqi, and some lackey fukkboy named Ahmed Chalabi, who nobody in Iraq even knew, and they could disband the Iraqi army in the process, and they would be greeted with roses as liberators for doing so.