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I think TT misunderstands what the difference of opinion is between FDA and the UCSF scientists. It is NOT the fact that the radiation is being deposited preferentially into the skin and immediately beneath it rather than spread through the body. The doses are being measured in "effective dose" which includes correction factors for the differing sensitivities to radiation of different organs, among them the skin. In any case, if I remember correctly, the skin is one of the least sensitive organs.
The key issue raised in the letter, and I don't see it answered by the FDA although I haven't looked through their references, is this: When low-energy x-rays deposit energy via Compton scattering, does it cause more breaking of molecular bonds, and therefore more cancer, per unit of energy deposited than higher-energy x-rays and gamma rays? (The "dose" is basically the amount of energy deposited per unit mass, to which various adjustments are applied to get modified versions of the dose such as "effective dose" and "dose equivalent".) As I said, I'm not an expert at all on the medical end of this, so it's possible that there is lots of research that answers this question, and if so it is undoubtedly discussed in the some of the documents the FDA references, but the FDA letter itself does not seem to address it.
The UCSF letter raises several other issues, but these are mostly lingering uncertainties that equally affect all discussions of radiation safety.
That said, the effective dose per scan of 25 microrems is really an extremely small dose. It's roughly your extra exposure to cosmic rays from sleeping on the third floor rather than the first floor for a year. Each time you fly across country, you are getting a dose from cosmic rays that is around 100 times greater. And you get that on every flight, while you only get scanned on a fraction of your flights. So even if the mechanism suggested by the UCSF scientists makes these x-rays 100 times more carcinogenic per unit energy than FDA thinks (and it seems unlikely to me that the number is as big as 100 because the number of photons per unit of energy can only go up so much before the radiation stops being an x-ray), the risk of the scan would still be less than the risk of taking the flight itself.
The point about proper operation of the machines is very real. The recent series in the NY Times about medical x-rays was scary.
I, as an occasional flyer, won't worry about being scanned if the machine is operating properly. I do want those machines carefully maintained and inspected. Avoiding unnecessary exposure of flight crews might be a good idea, especially if the UCSF argument is correct.