What's the difference between the Alu-Cab Roof Box and the Alu-Cab Wood Box, and can I mount it toward the rear of my roof rack?

There's no difference — Alu-Cab renamed the Wood Box to "Roof Box" as part of a website update, it's the same product. It can be mounted toward the rear of a T-slot roof rack; placement is mostly personal preference, though mounting it further back will increase wind drag slightly.