For what it's worth, my grandmother was a witness to the Port Chicago disaster, and slightly injured watching the event from her home, at the time near Pittsburg California.
I've bolded the assumption that I find problematic. There is no reason to suppose the WTC collapses all hit bedrock as a single, sudden impact. Quite the contrary. Losses over the side would have absorbed some of the energy before the main impact, the second "crush up" phase supposed by Bazant et. al. would have sustained it, and the "collapse front" is likely to have been somewhat diffuse as well. This is borne out by the Lamont-Doherty Earth Observatory siesmographs themselves, seen here, which both show diffuse events approximately eight seconds in length and peaking in displacement towards the middle of the record.
The Port Chicago disaster, on the other hand, involved nearly the entire contents of an ammunition ship plus the railhead nearby exploding almost at once. Your assertion that "less than half [was] perpendicular to the surface" is also misleading -- the bulk of explosives were contained in a ship, and much of that below the waterline. This blast would be transmitted through water, and thence to a dredged ship canal directly underneath, potentially as a single shock wave. It should be clear that the siesmic signal was much, much sharper since the event was shorter in duration.
The Port Chicago disaster also involved an estimated 5,000 tons or more of various explosives, perhaps 1,500 tons TNT equivalent. In contrast, I once computed the total gravitational potential of the WTC towers, using a round and possibly optimistic 500,000 tons of mass and a linear taper distribution, at 160 tons TNT equivalent. We further know that losses outside the footprint and destruction of materials absorbed a non-trivial fraction of the potential energy. This leaves perhaps 50 to 100 tons of energy at most to contribute to siesmic events, or halve these figures if you want to use your own pre-collapse mass estimate. You should use this estimate, not the total potential energy.
What you are arguing against is that the WTC cases seem to have been ten times (yes, only ten) less efficient at transmitting shock to bedrock than Port Chicago. Even neglecting the different phenomenology, which could easily explain the different coupling coefficient, you must accept that the Port Chicago incident was one to two orders of magnitude larger. There is no reason to assume siesmic propagation is linear with respect to the magnitude of an event on the surface.
Bottom line, this approach is far too crude to either confirm or deny a mere factor of two in the pre-collapse mass estimate. You should not leap to conclusions regarding Dr. Bazant's calculations, and your accusation is premature at best.
Your best argument regarding mass, in my opinion, is in comparison to other skyscrapers. Somebody has made an error or a significant asymmetric assumption, because either the WTC Towers were lighter than claimed, or the Sears Tower is heavier. Direct methods will be your best calculation approach. I don't believe you'll get anywhere approaching the problem obliquely, as in the siesmography, because it introduces still more simplifying assumptions and uncertainties -- clearly we already have too many.
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