If the two batteries are on different sides of the isolator, not a problem. They can be different sizes, brands, etc. as long as they have roughly compatible chemistry, e.g. both lead acid, and are only connected when charging. (Which, of course, is what the National Luna isolator is supposed to do.)
Batteries that are permanently connected together in the same bank, e.g., a diesel vehicle with two starter batteries, or the multiple batteries in a large camper battery bank, should ideally be identical.