The rules that you use to compose axioms and propositions are a different set of axioms defined by the Logic system you're using. e.g., can a proof consist of infinitely many steps? Can I use the law of excluded middle? Some logic systems won't let you re-use the same proposition more than once, etc,...

They're usually considered separate, because they're orthogonal to the foundational axioms you're using to build up your mathematical systems. With the exact same system of axioms, you might be able to prove or disprove certain things using some logic systems, but not others.