One, 3oz - did Chertoff go to his local CVS and saw at the travel sizes rack what sizes were available and drew a line? Odd.
My educated guess is that your speculation is closer to the truth than we really want to know.
Note - this does not address the general waste of time that is x-raying liquids. I certainly think that the xray machines - and the TSA guys reading them - are not going to pick out the gradient in densities of different liquids and then compare them to explosives densities and compositions. But, why a quart-sized bag? Again, just an arbitrary number, if it's laid out flat in a bin should it really matter what the size is?
I believe this is the TSA's attempt to minimize the impacts to the security lines when they start checking everyone's 3oz bottles. They just started feeling good about themselves because lines were moving really quickly because nobody was carrying on bags. Maybe someone on FT has some real-time experience, but, my guess is that some checkpoints will grind to a halt and lines will be huge. I expect the next bit of TSA social engineering will be for one of their spokesholes to come out and remind everyone that lines move quickly if you check your luggage when wait times increase dramatically.