Computer radios have adjustments they can make internally. End Point Adjustment is one of them. With that function, you can adjust the transmitter to tell the servo to move farther or move less. Unfortunately, it doesn't always work that way at the airplane. The best way to adjust your surface throws is to do it with the hardware in the model, and then use the radio to fine tune that. When you attempt to change the surface throws with the radio, the accuracy of the movement and the power from the servo can be messed up. You really do not ever want the transmitter to be trying to move the servo more than 100% for example.

Yeah, leave the radio set for 100% for it's throws and use 100% for full rates (whatever less for low rates). Set the throws with the connections at the horn and the servo. And fine tune with the radio. Truth is, don't fine tune, just go fly with the throws close to suggested and see what throws work better with your CG. Tune the CG and the connections in the model to get the response you wish from the airplane, and if you can't get the throws fine tuned in the model, THEN mess with the endpoint adjustments.

One of the biggest mistakes made with computer radios by the guys who think it's easier to setup their airplanes in the radio instead of when building happens all the time. They slap the pushrods into the airplane wherever and then start cranking the TX throws up over 100% when the connections have screwed the throws in the airplane. If you've got the servo arm connection in the farthest out hole, you're really not going to get appreciably more surface throw by going past 100% in the TX. All you're really going to do is screw up the feel of your stick. You wind up with what amounts to the same response you'd get from the stick being set with reverse exponential.