You're missing the point. There are billions of theists on this planet, and they remain theists because doing so is 'working for them' in some significant way. Theism is a conceptual paradigm, just like scientific materialism, is. And it's working for the people who embody it or they would seek and accept something that worked better. We humans are nothing if not selfish that way.
Not missing your point. But the OP was about the interference on the scientific method of atheist 'beliefs'...
That seems strange.
Methodological naturalism is a 'useful' conceptual paradigm, and has worked just fine for many theistic scientists.
The gap between atheism and methodological naturalism is effectively none, in terms of cognitive dissonance.