I have already purchased 8 men's shoe boxes from the container store (14-3/4" x 10-1/8" x 5-5/8" h ) and 2 boot boxes (22-1/2" x 14-3/4" x 5-3/8" h ).
I had planned on two shelves with 4 shoe boxes and the bottom shelf with 2 boot boxes.
Since you have boxes of two different heights and need dedicated shelves for each size I think you can go ahead and build the rack 48" wide. I even think you can use the less expensive melamine.
If you use expanded PVC then go with 1/2"
Either way, I would have vertical dividers cut to provide support to the shelves. Three dividers for the shoe box level and one for the boot box level. The height of these dividers would be the actual height of the box (without lid) plus whatever gap you want.
Use some leftover material for the back if you can. A full back adds weight but also strength.
Have the rack sit on the sides and possibly back. Don't have it just resting on the bottom shelf. Shim to keep things flat and square once the rack is done and setup.
Have some sort of support built into the middle underside of the rack. Something you can shim or adjust.
-----
Currently keeping:
6.10 Gonyosoma oxycephalum (Javan, mixed colors)
1.1 Philodryas baroni
1.1 Lampropeltis triangulum multistriata
1.0 Rhodesian Ridgeback