There are several motivations to the factoring of the build into extensions, and one is to be able to make the emscripten build less of a beast by taking basically all the extensions out. Because if the executable is fat as an EXE, it gets super fat when it goes through LLVM to make JavaScript. And there's no use to have PNG encoders for a browser that already has it, or FFI when there's no DLLs you could possibly call, etc.
In the past we've made %r3.js files that worked as experiments, so what we're looking for is something that's more than an experiment, which people might actually want to use.
So we are "working on it", but also working on it in the sense that rebmake has more configs. @szeng already added some LLVM support:
So I suppose we're not too many steps away from having an r3.js on Travis. It will happen when it happens.