Large water changes are more efficient than smaller ones. To say they're not useful is very inaccurate, even by the article you linked (which I read before setting up my automatic water changes). On average, they're about 4% less efficient if I remember correctly. For me, to oh-so-slightly decrease the inefficiency of automatic water changes, I pump new water directly in front of my return pump so it goes straight into the tank and take out just before the return water gets back to the return pump. How much effect does this have? I have no idea, but it makes me feel a little better. It HAS to be a lot better than having the removal and intake in the exact same spot as that would take a lot of new water out with the old, which would completely defeat the purpose.
I'm fine with them being less efficient. I hate water changes and am fine with doing a gallon or two per day automatically and having consistent water changes done as opposed to having 4% more efficient water changes, but having to spend an hour to do them. At the end of the day, my tank is looking much better with lots of small water changes than it was with no water changes, and that's a good thing.
Brandon