I've finally updated plonetheme.webpacktemplate for Webpack 2.x. I should be using it myself for the next few weeks, so I expect to solve any issues.
I'm also experimenting the related webpack plugin (one that loads resources from Plone RR for webpack) with add-on development https://github.com/plone/plone.app.theming/pull/130 Not sure yet, if it's really that useful outside theming.