Dear Hector,
The difference between mathematical models and the way nature really works, is precisely the point I'm making. Maths models of certain forms have mathematical restrictions that nature doesn't - maths can be incomplete but reality isn't - and we our free to fix our models by changing their maths form.
The Gödel connection is not as adventurous as it may at first appear, but does depend on a *very* careful meta-science analysis (review paper) of what it means to construct a scientific theory such that it accurately models the physical world. This is related to Einstein's point that he makes in the EPR scenario, but involves being *far* more careful about the specification of the 1-to-1 correspondence between features of reality and a mathematical theory - this is captured in my usage of physically-real term.
Precisely because of the points you make, the domain of applicability of Gödel's original incompleteness proof to science theories is restricted to causal dynamic systems that implement arithmetic changes over countable numbers of objects of different types. As long as the different object types are physically identifiable as being different types, then they can be classified into different sets in a mathematical theory, where the cardinality of the sets gives the countable number of objects present in the physical world (an accurate 1-to-1 correspondence). Note that ZF set theory is not the appropriate set theory for science theories as in reality objects occur as different types, and ZF doesn't support urelements or types.
The modelling of causal changes in object type A->B necessarily gives a form of logical implication in a 1-to-1 model of reality, and by carefully tracking the mathematical modelling of causal changes to the numbers of objects in reality, the conditions for when Gödel's theorem applies *within* a science theory itself (the critical meta-science bit is to parallel Gödel's meta-mathematics exactly) can be itemised. These conditions for the original form of Gödel's proof are very restrictive but can exist for real physical systems - I show that this condition can be used to divide physics into Object Physics (where it doesn't apply) and Agent Physics (where it does).
The axiomisation required to apply Godel's incompleteness to a scientific theory is limited to the core features required to denote different object types in sets, such that arithmetic over the numbers of elements in the sets is supported - this just comes from the axiomisation of set theory and arithmetic. Application of the proof to real scientific theories with further mathematical features - that are not necessarily axiomised - is then explicitly dependent upon the corollary to Godel's theorem: as long as the additional axioms don't change the integer arithmetic captured in the core set of axioms about object numbers, then Godel's incompleteness theorem will still apply. Meta-science analysis of a physical system can identify whether the arithmetic axioms would be changed by the extra mathematical features of a scientific theory without necessarily having to axiomise the theory, as all is required is to constrain what they *must not* be like for the proof to still apply, ie. they must not effect the integer arithmetic over object numbers.
Consistency in a physically-real scientific theory with a 1-to-1 correspondence with the numbers of objects of different types is then, as you say, the key issue. For a 1-to-1 denotation of object A in reality, the logical truth value of A (true) in the maths means that object A exists in reality, and conversely not-A (false) means that object A does not exist in reality. In this context of a 1-to-1 physically-real scientific theory of arithmetic changes in object numbers, an inconsistency in the theory would necessarily imply that a statement of the form, A and not-A, could be derived. This statement has the meaning that object A *both* exists and doesn't exist at the same time.
Now our observation of reality has been very time limited so far, and so an object existing and not-existing at the same time might arise, but it hasn't been observed so far. As this sort of inconsistency would imply that real magic was physically possible, the induction from our time limited observations of reality to a general statement of truth about reality seems safe - all science implicitly makes this assumption, otherwise the pursuit of science would be somewhat pointless. In a 1-to-1 physically-real scientific theory this gives the required form of consistency for Godel's incompleteness theorem to apply and for the theory to be *known* to be incomplete over arithmetic changes in object numbers.
In the 11D pure geometric theory considered for physics unification (STUFT), particles arise as topological objects that either exist or not, are of 12 different types (corresponding to the fundamental particles), and are countable. So when the full set of conditions for arithmetic changes in object number required by Godel occur, the theory is provably mathematically incomplete. But by changing the maths terms used in the theory, and including the observation of an undecidable wave property for particles, this restriction can be bypassed to give a scientifically complete theory. The notable feature is that this change - integer valued terms to real valued terms - gives a (meta-science) *derivation* of quantum field theory. As applications of Godel's incompleteness theorem go, it is hard to imagine a more significant and dramatic example.
Regards,
Michael