Thanks for being a guinea pig. I've been reading conflicting opinions on whether this method is safe or not with regular canister filters. The few pictures I saw using this method had Lifegard systems below, which are quite different in design.
Fluval makes its designer aquarium with bulkheads on the bottom for the canister. However, they do use tall stand pipes on both bulkheads. There has to be a reason for that. I'm guessing it's to relieve some of the water pressure? It's definitely not for cosmetic reasons..