RE: concentrated mass versus debris cloud: Certainly a large mass of debris falling at speed has enough energy to do a lot of damage, perhaps to crush the rest of the building. However, consider the following:
Envision a 50 lb rock versus gravel of the same mass - which would you rather have dropped on your head? (assume you are wearing a hardhat or some kind of minimal protective equipment)- odds are good that the rock would crack your hardhat and your head, while the gravel would likely just slide off, even if it rang your ears a bit.
Same principle is accepted with anti-tank weapons, a large (120 mm) solid projectile at high velocity will punch out a tank, while an equal weight of 0.50 cal machine gun rounds at the same velocity will do nothing to a heavily armored target. The structure can absorb the energy of the multiple smaller impacts much more easily, and may have time to elastically deform and recover before the next one hits.
Another point is that the broken-up mass is shedding pieces outside the building footprint as it falls, therefore reducing the total mass, and reducing the total energy by the amount associated with those pieces.
A paper from the demolition industry that attempts to debunk the WTC demolition theory offers the observation that 95 percent of the debris fell outside the building footprint. See www.implosionworld.com and click on the WTC report. They seem to have debunked their debunking with this, if true (and I don't know if it is) because it's unlikely for the remaining 5 percent of the mass of the top section to have crushed the lower section.
As you have correctly observed, the upper section will fall apart much more readily than the lower section. To the extent most of the literature deals with the collapse mechanism, it seems to assume the upper section remains relatively intact. Here's one article - note the reference to the huge falling mass:
http://www.civil.usyd.edu.au/wtc.shtml The NIST report also refers to "...a top section above the impact and fire floors that was also a heavy, rigid box." However, the more detailed WTC 7 analysis (that I have only skimmed at this point), shows anything BUT a rigid box falling, in fact it shows the building coming apart into pieces.
That said, I don't claim to know exactly what happened to the WTC 1 and 2. It is clear NIST had the tools to examine the entire collapse, because they did it for WTC 7. They just didn't do it for WTC 1 and 2, leaving these questions.