It can be the case that both:

- The physics of the universe can be completely modeled as computation, and

- It's possible to pose undecidable problems about the way the universe unfolds

This is intrinsic to the idea of undecidability even for Turing machines, e.g. "we equate computation with the functioning of Turing machines, but there are real processes executable in Turing machines that are undecidable".

Of course, if our universe is undecidable it must be the case that computable processes can be executed within it, and it might be the case that all of the processes that are ever executed within it are computable... but it might be that some of the processes that are executed are not computable... because the machine may.. or may not?