The exhaust rubbers will soon split if they are much out of alignment. They are designed to allow a certain degree of motion, but if mounted in a bias, that motion will continue beyond their designed range. Unfortunately, the lack of precision in the bends of most aftermarket exhaust pipes and mufflers, coupled with fatigued isolastics can make it difficult to mount the mufflers without stressing these mounts.
I always assemble everything loosely, tighten the muffler mounts, then tighten the exhaust rings at the head and finally the muffler/exhaust pipe clamp. If I cannot make things fit without deflecting the mount, I will either bend the pipe slightly or as a last resort, elongate the mounting holes.