I keep seeing a lot of advice that waterproof mattress protectors should never be used above the shoulders of the infant as they need to be able to breath through the cot mattress if they should roll in the night. Is this true? If so, do you have suggestions on how to keep the rest of the mattress sanitary?

Red Nose recommends the following:
......always make sure that the waterproof mattress protector is strong and a tight fit.
Never put soft bedding under the bottom sheet, such as a sheepskin, as this makes the sleeping surface too soft.
https://rednose.org.au/article/what-is-a-safe-mattress

By about 4-5 mths of age most babies will be rolling & many prefer then to sleep on their tummy.
A cot mattress should be firm, clean,well-fitting & flat.
This is what will make the environment as safe as possible, particularly when baby starts to roll.
As long as the waterproof mattress protector is tightly fitted & not loose,soft or padded (ie doesn’t take away from the firmness of the mattress) it would fit Red Nose guidelines.