The mapping exists, just not necessarily within the language; the CTT is orthogonal to practical difficulties of massaging the data into a usable input format. (e.g. how to convert a binary tree in to the TM's format and vice versa)
>The Church-Turing thesis says absolutely nothing about abstraction barriers your language might enforce, e.g., what you get if your language has parametric polymorphism ...
Those all speak to the issue of how difficult it is (for e.g. a human) to implement the function, not whether language/computation model can compute it at all.
>Compilation translates programs in a source language into semantically equivalent programs in the target language. Compilation doesn't guarantee that every target language program is expressible in the source language - in fact, this is often not the case.
If you have a computation for which no TM (or asm, C, etc program) exists that computes it, let us know! That would be real progress on the CTT towards a negative answer and a Fields Medal for whoever found it!