Sure when targeting the web with software that doesn't exist yet I would definitely write that in JS. However, if there is a well-tested crypto library that has 300.000 lines of well-tested C code and that I can use without too much pain by transpiling it to JS I'd always prefer that to writing my own implementation in JS. In that sense transpiling is a great way to reduce redundancy by allowing to use code in different context. Concerning the intermediate form: I'm a big fan of model driven development but I think our tooling for it isn't good enough yet, so until someone invents a description language that is really powerful enough to describe let's say a crypto library and then generate code from that in various languages I think transpiling from one concrete language to another is still a better option.

BTW a lot of the power of Python, Ruby and JS comes from the interface these languages provide to existing C/C++ codebases, and I assure you that the binding code to make this work is often far from pretty. As end users we don't care about this though as long as it works.