Methodological naturalism is considered a strategy for conducting natural science, in which naturalism is temporarily assumed but not affirmed as a metaphysical reality. But for those who reject metaphysical naturalism, it is unacceptable to assume a falsehood for any purpose, except to prove that it leads to absurdity. For example, it would be nonsense for a mathematician to assume “1 = 2”, prove a theorem, and then return to “1 ≠ 2” because that way one could prove any and every statement.
What is reasonable is the bypass, which works like this: transform the problem, solve the problem, then reverse transform the solution. See Bypasses: A Simple Approach to Complexity by Z. A. Melzak (Wiley, 1983). Symbolically, this is S-1TS where S and S-1 represent the transform and its inverse and T represents the operation in the transformed domain. This is also how an analogy works.
A simple example is the technique of completing the square to solve a quadratic equation: start with equation ax² + bx + c = 0, transform it into a square (x + b/2a)² = –c + b²/4a, solve this by taking square roots, then transform the solution back.
The bypass works for a one-to-one transform because it is invertible, but it does not work with a one-to-many or many-to-one transform because they are not invertible. Since the transform “1 = 2” maps 1 and 2 to the same number, it is not invertible and so won’t work as a bypass.
Something similar is at work with the attempt to use methodological naturalism as a bypass: reality is mapped to “nature” by either excluding anything non-natural (supernatural) or by mapping anything non-natural to something in nature. The former transform is clearly not invertible but the latter is not either because it means that something in nature has two sources or explanations, one natural and one non-natural, which is a many-to-one mapping.
There is an alternative method available, which could be called methodological creationism. It transforms everything natural into its corresponding creation and every supernatural into an act of the man Jesus of Nazareth. This transformation can be inverted since it is a one-to-one mapping. For example, organisms can be mapped to creatures, which can be reversed mapped at the end. Non-natural acts of creation can be mapped to acts of the man Jesus of Nazareth, which can be reverse mapped at the end.
An advantage of methodological creationism is that creative acts are no longer in a separate domain from everyday reality because they are mapped to the acts of a particular human being, whom people can know or read about. One need not speculate about the actions of a mysterious spirit being but may reference the actions of a particular man, and so have reasonable expectations about what this man would or would not do. This allows a systematic science to be built up by the usual scientific methods of data collection, inference, hypothesis, and testing.