On most mathews when your bow is PROPERLY paper tuned your rest will actually be to the right of center. As others have said, your sight has nothing to do with tuning. the bow shop owner is clueless. If possible, you could build your own paper tuner and do it yourself.
However, speaking for the owner of the shop. Perhaps what he meant was that if he moves out the sight and your adjust your rest accordingly, the bow would be out of tune. When your sight was into the riser where were your arrow hitting? Good Luck