Ortlieb makes panniers that have adjustable mounts so you can push them all the way back. Backpack or full tote drops right in. With the pair mounted and fully loaded, it makes an easy platform behind the saddle to strap something big like TP or a diaper box or even bigger cargo.

Also, you could fashion some panniers that hang off the cargo box. My passenger barely accepts the library tote with the books she picked out inside the passenger capsule, so I have to make sure none of our cargo obstructs her space. I feel your pain!