In the long run both branches appear to be lower than you will want permanently. Deer will browse anything they can easily reach. Doesnt hurt to leave them now as they will help increase the caliper of the tree, just keep them from competing to become the central leader. Either pinch the growing tips out of them or bring them more horizontal.
Once the CAR spots occur nothing can be done about the spots. CAR spots on apple leaves do not create more spots on other leaves.