My build process is automated, so it's not a huge darn to me if my computer has to run one additional program once in a while. It's running dozens of them all the time. And if you find CoffeeScript creates a lot of JavaScript bugs that aren't in your CoffeeScript source (adding "another layer of indirection to obfuscate bugs"), I think your experience is atypical.

And as for "obtrusive," I guess that's just subjective.