For compatibility. Everyone is moving toward ES6 modules, so if you write your app in CommonJS now, you'll likely have to re-factor it into ES6 modules in the future.
Not a deal-breaker, but it's certainly needed (and it sounds like Node devs are well aware of this).
But yes, you're correct that it will be years before CommonJS is removed, if ever. Although I could see it being tagged as deprecated in the next few years.
I personally would have been totally fine with CommonJS on the frontend, as a longtime browserify user. Almost wish that had happened simply to avoid the transition to another module system for the Node ecosystem. But es6 modules do have certain advantages for the frontend, like making tree-shaking easy.
Of course; Typescript compiles in such a way that Node understands what was intended, it would be nice to compile to ES6 directly. Typescript is ES6 with types. A small change, essentially ignoring types, would require so little processing that it could probably be done live as if it were reading pure ES6.
I think that's within the realm of possibility but would require Node to understand ES6 in its entirety.
I agree that getting ES6 modules in the browser will be nice, in the end, I see it working in practice a lot like it's implemented in Babel, to work with CJS modules.