I'm not sure what you mean by "standard tooling for every language." Cog will work with any text file. Or do you mean that cog itself is non-standard?
I like the idea of everything sharing the same file, too, but it does make working with Python part a bit more difficult.
Also, with keeping it separate, the "every language" part comes up. It doesn't have to by Python if it's a separate code generator. Whatever suits you will work. You can generate code for C in C++. Or assembly in Common Lisp. Everything in anything.