Yes, having the control horn place properly on the control surface is important. Having it incorrectly placed won't necessarily give more or less throw, but more often than not it changes the geometry of the throws. Usually giving you more throw in one direction and less in the other. The holes in the control arm need to be placed directly above the hinge line for that control surface. See the attached diagram to get a better idea of that I'm talking about.

Hope this helps

Ken