Closed source miners generally perform better then Ethminer. You'd be surprised how much a 2% fee incentivizes these miner devs to make their miners as competitive as possible
You are right, 1-2 percent is big money. The commission deduction for my system is equal to a gain of ( %1) 1.8 mh / s. When I try Teamredminer, if the difference is 3-4 mh / s, then I am profitable.