Actually, it says "Some of the earliest warnings of the attacks of 11 September were mobile phone calls from passengers", hence we cannot know from this text, if the pilots were able to use the transponders. It might very well be that they were unable to use them, for the kidnappers may have prevented that.Satori said:
The detonation at the bottom was a hoax, for what I know. Please read this about that issue.
You can find some videos on this page. Don't be fooled by the attempt of a "scientific" explanation, though. BTW, they hint that "each floor was wired to a separate detonator". A lot of explosives would have been needed for that.
For a better explanation of what happened (IMO), you should visit ImplosionWorld.
Some excerpts:
"DID THE WORLD TRADE CENTER TOWERS ACTUALLY ?IMPLODE??
No. They collapsed in an uncontrolled fashion, causing extensive damage to surrounding structures, roadways and utilities. Although when viewed from a distance the towers appeared to have telescoped almost straight down, a closer look at video replays reveal sizeable portions of each building breaking free during the collapse, with the largest sections--some as tall as 30 or 40 stories--actually ?laying out? in several directions.[...]
WHY DID THEY COLLAPSE?
Each 110-story tower contained a central steel core surrounded by open office space, with 18-inch steel tubes running vertically along the outside of the building. These structural elements provided the support for the building, and most experts agree that the planes impacting the buildings alone would not have caused them to collapse. The intense heat from the burning jet fuel, however, gradually softened the steel core and redistributed the weight to the outer tubes, which were slowly deformed by the added weight and the heat of the fire. Eventually, the integrity of these tubes was compromised to the point where they buckled under the weight of the higher floors, causing a gravitational chain reaction that continued until all of the floors were at ground level. "
Just kidding. But like I said, I still need to review all of the info. more in depth. 
