How does your workflow looks like with react.js along with backend?
I have usually solved this problem (duplicated index.html/php file) using this webpack plugin: https://github.com/ampedandwired/html-webpack-plugin
The idea is the opposite of yours I think. Instead of compiling your php files into static html, you can use the HtmlWebpack plugin to output a index.tmpl.php file (or whatever extension you need) using the filename configuration option. Normally I set that path to be the templates folder of my application server.
I believe this approach is generally easier than doing the other way round.Using this plugin has other benefits, such as automatic bundle script tags injection depending on your Webpack output config, and automatic cache-bursting file hash added to the script tag urls.