I think a much more logical answer would be that she took 48 so that no matter what, all equipped Materia, which is a max of 16 per character for a total of 48, (see where I'm going with this?) which is, presumably your BEST Materia since you have it equipped, is taken at the VERY least. I guess a way around the handicap imposed by this is to make sure all equipped Materia sucks, and that your best Materia are last in the inventory screen.