I have never been able to figure out exactly how there arguments for methodological naturalism are supposed to go. It seems that a lot of the time this sort of thing just gets asserted without an real explanation of why it has to be like that.
Let's take the subtitle of Richard Dawkins' book The Blind Watchmaker, which is "Why the Evidence of Evolution Reveals A Universe Without Design." Now, if this is taken seriously, it has to imply that evidence of evolution could have revealed a universe with design, but it just didn't. Otherwise, what leads us to the conclusion that the universe is without design wouldn't be the evidence of evolution, it would be the constraints of rational inquiry. The evidence of evolution would be superfluous
Russell presumably said if he met God and were asked to explain is failure to believe in him, he would say "Well, God, you didn't give me enough evidence!" But, that wouldn't make a whole lot of sense unless God could have given enough evidence, but just didn't. But, if it is a fundamental principle of reason that we can't possibly have evidence for God, then that's kind of empty don't you think?
I once asked a longtime friend who is now a well-known atheist philosopher, Keith Parsons "If I were God, and I wanted to rationally persuade you of my existence, what would I have to do?" He told me that if I, as God were to make the galaxies in the Virgo Cluster to spell out the words "Turn Or Burn, Parsons This Means You," he's turn. I guess for many naturalists, there are limits on methodological naturalism. But if Parsons were to turn, I am sure at least some of his atheist colleagues would accuse him of succumbing to a God of the Gaps explanation.
If MN is stated strongly enough, it requires you to reject a theistic explanation (which is surely logically possible) even if it were a true explanation. That's a position that I would describe as radical naturalistic presuppositionalism. Are there any naturalistic presuppositionalists out there? Are there Cornelius Van Tils in the naturalist camp?