A long read, but this post by Dan Abramov illustrates how React Transform currently works, its shortcomings, and how a new approach is likely to remove all of those shortcomings.

If you're using Webpack and React (and who isn't, these days?), and you're frustrated that the functional components you've been encouraged to use aren't supported by hot reloading... the last section here presents the (relatively short) roadmap to the solution.