It's important not to mix everything. CoffeeScript is a language. There just happen to have an implementation for it.
This invalidates the "debug" workflow problem. Let me restate the CS debugging workflow:
Start discovering the problem in the code I wrote.
Fix it in the CS
Problem fixed, move on, otherwise start over.
A computer language is by definition a mean to express unambiguous statements. So does CS. So does the other languages. The resulting program will do exactly what your code asked to.Do we check compiled code when we code in C? Do we look at the Bytecode when we write Java?
The fact that CS compiles to JS is an "implementation detail". That's the CS compiler's job. If you don't trust it, don't use it.