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I don't think we will ever understand everything, at least not with the cognitive capacity we have today. And even if we did, there would still be a large group of people using God to explain phenomena either because of ignorance or other reasons.

For example, people still say "good" behavior is evidence of a higher power even though there's perfectly fine naturalistic reasons that people are good; most people simply haven't considered them for whatever reason. And if the mechanisms behind certain phenomena could be explained, people would still turn to God to explain "why" those mechanisms in place. For example, when people discovered that the Earth revolved around the sun and gave only an illusion of the sun rising, people still credited God as being the underlying force that causes the mechanism in the first place.

But for questions like "why does the universe exists?", I don't think we will ever be able to answer that. Will people continue to use God as the "explanation" (I use the term "explanation" very loosely) for questions like that? I don't know.