So, correct me if I'm wrong. You're asking why the intake of the filter (on the canister) is on the bottom and the pump head is on the top? Best I can figure is to *possibly* save on ~1' of head pressure. Doesn't really make much sense though, canisters should work as a closed loop and most of the vertical head pressure should be negated because of the siphon effect. Basically that means they only have to push against the elbows and from the level of water to the top of the tank.
You're not wrong, that is what I'm wondering about. Also, my thoughts echo yours about cannisters being a closed loop... siphon lock = neutral flow. Pushing water up through filter media isn't specific to closed loop filters, however - epond might have it right, this may just be a case of heavier debris staying at the bottom.
I noticed the AquaClear HOB I purchased forces the water up through the filter media. I've also spotted some DIY wet/dry sump systems do this with passive flow instead of forced. TopFin filters avoid gravity altogether by having the water flow sideways through the filter.
I thought at first it might just be a gimmick or patent issue, but that wouldn't explain the DIY examples. If it had practical purpose, I would work it into my designs.