There's still react-scripts-ts [1] which drops the majority of Babel in the CRA pipeline for solely Typescript. Presumably, it will remain active as it is still a useful alternative if you know you are going to want Typescript from day one. (This Babel-based support is perfect for those unsure and looking to experiment, which is great.)
create-react-app is built on Webpack, for hot module replacement (HMR), and that requires a webpack loader. There's babel-loader and ts-loader. The stats in the projects are similar, but babel-loader is part of the babel project while ts-loader comes from an independent project, so it may be better integrated. Also ts-loader suggests using it with babel-loader. I'm not sure why, but if you install ts-loader and babel-loader you'll wind up with more dependencies than if you just install babel-loader. https://github.com/babel/babel-loaderhttps://github.com/TypeStrong/ts-loader
The last I checked (a month or so ago, but before the recent 2.0 release) create-react-app didn’t have hit module replacement. It just watched files and completely reloaded the browser when anything changed.
[1] https://github.com/wmonk/create-react-app-typescript