I saw an interview with Hawley. He claimed that they did a study on the type of explosive they were concerned with, and then determined that the combination of 3oz bottles and a 1 quart bag would not pose a threat. I suspect that you could do the math and figure out how many 3 oz bottles you can fit in a 1 quart bag to figure out the maximum amount of liquid they want to let through. If people were allowed X ounces in any combination there would be massive confusion as most people can't seem to handle simple math.

And putting it all in a single bag makes it faster for the screeners, because then any liquids they see on the Xray are clearly not in the bag allowance.