typically generate enough energy to heat the large structural members to the point where they would fail;
The structural members wouldn't have to fail. As they heated they would lose more and more of their integrity. As they sagged it put more stress on the bolted connectors.
---have fire suppression systems (such as water sprinklers) that would further inhibit the fire from reaching anywhere near the heat necessary to create a total collapse;
Most, if not all high rises have utility chases that are generally part of the elevator framing. This includes the mains for sprinkler systems. It's not a stretch to believe those mains were sheared, on impact.
the structural members are protected by fireproofing materials, which are designed to prevent the structure from reaching failure temperatures within specified time periods;
That fire proofing is spray on,light cement. I can imagine that much of it would shatter under the of a 767 travelling at 550 Knots.