Babel makes it possible to do compilation that TS doesn't do. E.g., you can use esnext language features that TS doesn't support, like do expressions. You can also use babel plugins that add utility, like the Babel power-assert plugin.
The only counter-example that I know of is that async/await were initially only supported when transpiling to ES6, but this is not true since at least 2.2 (https://github.com/Microsoft/TypeScript/issues/5210).