A very interesting post, Rebecca. I too have noticed that Chuck's fly pupae (anyone's I imagine), vary in size. There are several possible reasons for this. Remember that in nature, flies, like everyone else, are there to reproduce, not win a place in the Guinness Book of Records for their size, so size in itself does not make any difference to the success of the species.
The easiest way to produce a supply of pupae of the same size is to remove the breeding medium a day or two after the flies start laying, so that the larvae are about all the same age. (I never do this myself. It is extremely wasteful of medium). With a homogeneous population like this, you can grow maximum sized flies by letting them pupate when they are ready, or produce smaller pupae/flies by "flooding" the medium with water before the maggots are ready to pupate. They will flee the water, which would drown them, climb to a drier area, and, without food, pupate, producing smaller flies.
I have chatted with Chuck about the problems introduced by the changes made over the last year in dry dog food (beef and lamb meal are out; chicken is in) and the considerable effort that he has expended in trying to make an optimal feed mix, adding things like carotene and one egg to every 5 gals of medium (!). I suspect, though, that in this case, the smaller pupae represent a shorter growth period due to higher temp. I shall call him tomorrow, and then make a post explaining why I was wrong!
Fortunately, Chuck sells his pupae by weight, so if they are smaller, you get more per gram!