If your oil filter has so much debris in it at 1 or 2 thousand miles that it triggers the by pass then you have serious problems. It will let you know very quickly when it grenades.
I believe you may actually get more oil out of the pan with the extractor than the fumoto. I own an extractor for my wife's Audi but I still dump my oil the old fashioned way on my other cars. A disposable glove fixes the mess problem.