If I understand you correctly you are comparing your homemade pepsi can stove to a professionally built (and optimized) Zen Chimney stove. Seems reasonable to me that you couldn't be a pro... I know I wouldn't be able to.
The longer burn time, means lower flow rate out of the stove and it allows for greater time for the water to absorb the heat. That (in general) makes the stove more efficient.
BTW, I built an excel spreadsheet for some people in the community to calculate stove efficiency. I got a bit carried away and ended up with what I consider a pretty refined tool. Here it is if you are interested:https://drive.google.com/open?id=0BwVBql46i9hbUE9HUm0xN3MwTWs