Where did the thermite go? Was it applied directly to the steel? There would have to be a noticeable amount on the building, wouldn't there? Wouldn't it be obvious if someone brought in chemicals and coated trusses with them? Not to mention that simple remote detonators are difficult to set off thermite reactions. Also, the planes probably don't have the skill to point the aircraft at specific points on the buildings, so they'd have to coat most of the building with it.