We can still test the theory that computation describes physical reality with experiment (presumably it makes predictions). The scientific method still holds.
The theory of general relativity answers this exact question. It has been tested experimentally and has been found to be correct in the classical regime. By correct I mean that the experimental data agrees with theoretical prediction.
Yes, these are all our attempts at explaining the nature of reality. A kind of reaching into the unknown. A desire to understand the universe and our place in it.
The universe as a computer/computation has been explored by many (e.g., see John Wheeler and Seth Lloyd). However, the laws of physics give us a lot more predictions, so their explanatory power tend to be greater. For example, the nature of space and time.
A related question might be, what's the difference between mathematical (Godel), computational (Turing,) and physical (Yang-Mills) undecideabilty/computability?
A quantum Turing machine would be needed to simulate a truly quantum process. Stochasticity exists in classical systems, but that's an entirely different type of randomness.