That issue is back from when Babel was still called 6to5.
Babel didn't support JSX, decorators or type annotations. Now it does. Babel 6 is even more modular, lending itself even more to extension than Babel 5 did before.
There's nothing stopping MS from adding TS extensions to Babel.
Also TypeScript existed before Babel and there are some features not supported by Babel (modules, public/private). See this issue for more details https://github.com/Microsoft/TypeScript/issues/1641