Please do go bare botton with a puffer. You will not only be removing a lot of surface area for bacteria to colonize on (puffers need all they can get) but they will be freaked out by the unnatural appearance of their surroundings.
Bare bottoms really do freak them out- when adding water to my red eye Nikita's tank, I moved the gravel and created a bare spot. Didn't notice it right away but she did- she was staring at it and trying to bite the puffer in the reflection.
How tall is that? Can you reach the bottom? More water always equals better dilution but larger footprint equals more swimming room. Maybe you'll get a lazy fahaka like mine, who mostly hangs out in his cave all day.