I thought that exact thing when I did mine. Here's what I did:
**First, I should mention that the pump I chose was able to run in-line, or externally, thus not having to have the pump in the filter, and being able to add the C02 to the canister, which is after the pump. This eliminates "airlock" **
Instead of having the inflow at the top and outflow at the bottom, I had mine switched around. It has it's pro's and cons, but as long as everything is air tight and secured, it shouldn't be a problem to do it this way.
The reason I chose to do it this way, was because I knew I wanted to incorporate my C02 injection through the canister filter to maximize diffusion, it also makes room in the tank from any diffusers not being there (can make a huge difference in nano tanks).
I made a separate insertion on my bucket/container, right next to the inflow insertion. I chose to put the both the C02 line and inflow line on the bottom for two reasons.
1. If it's by the inflow, the C02 must travel throughout the filter, thus creating better diffusion.
2. Gas is lighter, thus it will attempt to rise, and going with the flow of the water, the C02 will be more inclined to being "forced" upon something in the filter, hopefully dispersing it throughout the water more effectively
Like I said, as long as everything is nice and air tight, and building integrity was not sacrificed for sake of time, then there should be no problem having inflow at the bottom and outflow at the top.
I was also thinking of incorporating a smaller, simple HOB filter, who's only media was either more polishing pads, or more bios.
I mainly use HOB's for surface tension so oils don't build up on the water surface.
If you were to put the outflow of the canister filter leading to the inflow of the HOB filter, the C02 dispersed water would travel through the impellers of the HOB filter, possibly dispursing the C02 even further.
At one time, I also just had the canister filter separate from C02, and just had the line from the DIY C02 bottle running to the inflow of the HOB filter and using the propellers on that for my only means of dispersion.
Both of those last two techniques could be argued against however, arguing that alot of C02 would escape as it leaves the HOB filter.
Either way, just giving my input on possibly making that nice DIY canister you made more effecient. =D