Source: I spent years developing with GWT
IMO transpilers are a Faustian deal. That's what my experience has taught me, your mileage may vary of course.
But I am not here to argue specific examples. Sure, I definitely agree with you that Javascript is the worst offender in the transpiler world. I do however not see the connection between using a transpiler and having it easy when refactoring. If you mean that the transpiled language has an easier to parse AST and is thus much more prone to automated refactoring (Eclipse's "Rename Method" for example), I won't argue that; I know it can be true.
Nothing of what I said will stop me from trying Elm (transpiled to JS) for a hobby project though.