Mister Captain, will your ship sink?

This is unfortunately a situation in which there is no systematic approach, and every high-ranking official's form of address will need to be learned / memorized individually. (Note that as part of the culture for most English speaking countries, you will use a person's name except in situations where the person has a very high official rank)

That said, I suspect that the "Mr/Madam President" form of address likely uses "Mr/Madam" to emphasize that this is neither a title of nobility, nor a rank of military, nor a member of the clergy. "Mister" is usually a common form of address (eg, "My friend, Mr Rogers"), so its use here is to distinguish it from other uncommon forms of address. But even knowing this, you cannot necessarily apply it as a rule to other situations.