This is indeed what the Offset Position is for. You set the Offset Position and then turn the Goto Offset Signal on. The thing you must remember is, if you are using the AXFOLLOW instruction, it is a requirement that your following axis be faster than your Master Register. In other words, that axis must have a faster Maximum Velocity and Accel/Decel rates. Otherwise, it cannot go to the offset you tell it to go to.
To answer your question, no it does not offset the Master Register location at all; that remains exactly what it is. It merely offsets its own CurrentPosition.