Even a seemingly perfect size can cause rubbing when the boots are brand new. This is because the rear captivator is manufactured to exactly the same shape for every boot and needs reshaping to the individual hoof.
Break the boots in gradually – or reshape the captivator with a heat gun or boiling water straight away, in which case neither breaking in nor protection is needed. Horses have different skin sensitivity, and the boots need to mould to the hoof.
If needed you can use Endurance Gaiters as a buffer between the plastic and the skin during the break-in period.
A correctly sized, correctly set boot should not rub. If you notice ruffled hair in the coat, which is the first sign of rubbing – document where it has ruffled and reshape again.