The break between theism and secular rational modernism is a relative not a radical one. Truth replaces God, scientific reason replaces revelation, scientific authorities replace theologians and the nature of heresy charges, but crucial aspects of the fundamental logic do not. The origin goal is still singular and universal; there is still a royal road leading from and to it; and the enemy for both programs remains, strikingly, "superstition". That is, in this context, unlicensed (that is, wild) enchantment. It follows again that, as against enchantment, both religious and secular universalist programs are different versions of the same road, with its two branches. They constitute, in effect, "two vying monisms", and the noisy, tediously predictable "debate" between the so-called "new atheists" and religious fundamentalists is largely a turf war for control over "knowledge, rule, order".
That said, there remains an important difference in principle between theism and secularism. It results from the apophatic nature of God as an ultimately unfathomable spiritual mystery, which denies the final promise of analysis and control that material reality, ultimately limited even if very complex, seems to hold out to science. Theism thus denies what scientism embraces: the prospect of ultimate mastery, and with it complete disenchantment.