I am not up-to-date on the bleeding edge but that explanation doesn’t seem correct? The use of x-rays in analytical chemistry is for elemental analysis, not molecular analysis. (There are uses for x-rays in crystallography that but that is unrelated to this application.)

At an elemental level, the materials of a suitcase are more or less identical to an explosive. You won’t easily be able to tell them apart with an x-ray. This is analogous to why x-ray assays of mining ores can’t tell you what the mineral is, only the elements that are in the minerals.

FWIW, I once went through an airport in my travels that took an infrared spectra of everyone’s water! They never said that, I recognized the equipment. I forget where, I was just impressed that the process was scientifically rigorous. That would immediately identify anything weird that was passed off as water.

Yes. The first step was upgrading to the new machines, now the size limits can be relaxed.