The relation of Gödel's Incompleteness Theorems to the Church-Turing Thesis
Here is a philosophical answer that may entertain you.

Gödel's incompleteness theorems are about the formal system of Peano arithmetic. As such they say nothing about models of computation, at least not without some amount of interpretation.

Peano arithmetic easily shows existence of non-computable functions. For example, being a  classical theory expressive enough to talk about Turing machines, it shows the particular instance of excluded middle which says that every Turing machine halts or runs forever. Nevertheless, from the work of Gödel an important notion of computability arose, namely that of a (primitive) recursive function. So it is not the theorems themselves that connect to computability, but rather the method of proof which establishes them.

The gist of the incompleteness theorems can be expressed in an abstract form using provability logic, which is a kind of modal logic. This gives the incompleteness theorems a wide range of applicability well beyond Peano arithmetic and computability. As soon as certain fixed-point principles are satisfied, incompleteness kicks in. These fixed-point principles are satisfied by traditional computability theory, which therefore falls victim to incompleteness, by which I mean existence of inseparable c.e. sets. Because the provable and refutable sentences of Peano arithmetic form inseparable c.e. sets, the traditional Gödel's incompleteness theorems can be seen as a corollary to incompleteness phenomena in computability. (I am being philosophically vague and your head will hurt if you try to understand me as a mathematician.)

I suppose we can take two stands on how all this relates to the informal notion of effectivity ("stuff that can actually be computed"):


For all we know, we are just a rather large finite automaton, capable of contemplating fictional super-heroes called "Turing machines" that are able to calculate with unbounded numbers (gasp!). If this is the case, Gödel was just a very good story-teller. How his stories translate to effectivity is then a matter of some (necessarily inaccurate) application of imagination to reality.
Because incompleteness phenomena arise naturally in many contexts, and certainly in all reasonable notions of computability, we conclude that the same has to be the case for effectivity. For example, suppose we could send Turing machines into black holes to compute a la Joel Hamkin's infinite-time Turing machines. This gives us immense computational power in which the halting oracle is a kindergarten toy. But still, the model satisfies the basic conditions that allow us to show the existence of inserparable sets. And therefore once again, computation is not all-powerful and incompleteness is a fact of life.