It may be that God may have developed the human brain in a manner that allows Him to communicate with the human mind through stimulation of certain neural circuitry. To use a metaphor, it may be that the neural circuits implicated in religious experience are conduits or "antennae" of sorts for a transcendent source, rather than the absolute point of origin in themselves.
Re: skepticism and materialism were clearly the default for every rational thinker and that those that dissent are poor mistaken unfortunates who may come around one day with enough patience. The concept of subconscious presuppositions in motivated belief cuts both ways for both theists and skeptics.
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