Using all the same size box does have a lot of advantages. If you can handle the weight of the deep boxes there is no reason not to do it. I have some ply wood deep boxes I used 3/4in and just used a dado joint. Painted them well and so far have not had any delamination. You will not have that much waste using a 1x12in board. You will end up using most of the drops for bottom boards, cleats, and stuff like that.