Naturalism vs Supernaturalism

Two difficult questions:

(1) Many cultures have existed, and many have died out, and many of them have written books on spiritual themes. Why is the Christian bible (or Hebrew bible or Muslim Quran) true whilst the others are not? Why do any of them have to be true? Why is the Judeo-Christian God real? Why not Zeus, or the tooth-fairy?

(2) How do we know that the ad initio position of the scientific method that explanations of the world (derived through science) can only be naturalistic/material (thereby discount anything supernatural). How do we know that position (though necessary for science to exist at all) is not flawed to begin with? It is even possible for science (through empiric experimentation to confirm or disprove testable predicted hypotheses) to show that alleged supernatural phenomena do not exist, when that is a foundational pre-requisite assumption?