Dear Ken,
I think there is a conflation between computational models and mathematical representations. It is true that mathematical representations almost always turn out to be computable models, specially when used numerically to approximate the solution to a real-world problem. But a mathematical model doesn't always come with its implementation (in fact rarely does). That is, one has to find a computer implementation for a mathematical model. There is no one-to-one correspondence between models and algorithms. For example, many Turing machines can compute the same computable function, but each can do so in a completely different way (e.g. a function that can be computed in linear time can also be computed in exp time).
While I may agree that the working assumption of science is that nature is mathematical I think it is far from obvious that science assumes that a particular implementation of a mathematical model is the specific way nature operates. This is also a common conflation when people think that saying that a natural process is Turing computable means that it is computed exactly by something like a Turing machine (nobody thinks the brain is a Turing machine, but most science works under the assumption that the brain is Turing computable, which is completely different). In your essay you point out Seth Lloyd's claim that the universe is a computer, this illustrates my point, because in fact Seth Lloyd does not think that the universe is a Turing machine, but in fact a quantum computer, which in the light of your own arguments I find difficult to reject.
On the other hand, I don't think that physicists will ever be able to close all loopholes in quantum theory at the same time, and it hasn't yet been done. While your ideas are provocative I still find the computable ground less subject to particular interpretations.