If you take a tape and measure from axle to axle and mark the physical center of the string, then use a bow square to split the berger hole, you'll see for yourself that that rest mounting hole and your center mark are not in the same place. To my knowledge there is not a bow made that mounts a rest so as to have the nocking point physically centered on the string. It's always somewhere just above center. How far just depends on which bow.

Why do you need to raise the rest? If you need to to get broadhead or fletching clearance for the shelf then by all means do so. As you are saying, you'll have to raise the nocking point (loop) a like amount to keep the arrow square. But you may need to tweak your tune a bit.

Don't forget that if everything on the string is set up for you then you'll most likely need to raise a kiieer button and peep the same amount. The sight too, but this can be done by shooting the bow and gang adjusting the whole sight, if you're using pins.