Well, if we forced our presuppositions on our experiments we would not have discovered gravitation, electricity, relativity, quantum mechanics, etc. Each of those advances is a metaphysical paradigm shift over previous views of reality. E.g. the original materialism was the billiard ball model with a random swerve, due to Epicurus. No one believes in the original materialism anymore, since it has been falsified in so many ways. Instead, we have redefined materialism to include a whole host of causal forces that were previously ignored or unknown.

Similarly we can mathematically and empirically differentiate between halting oracles and Turing machines, so why not leave both possibilities open as scientific explanations, instead of doubling down on the Turing machine model? Call halting oracles materialistic if it makes you feel better.