Kinda defeats the purpose of CSS modules but if you want to use (raw) Bootstrap alongside with CSS modules here you go:

webpack.config.js

 // "postcss" loader applies autoprefixer to our CSS.
 // "css" loader resolves paths in CSS and adds assets as dependencies.
 // "style" loader turns CSS into JS modules that inject <style> tags.
 // In production, we use a plugin to extract that CSS to a file, but
 // in development "style" loader enables hot editing of CSS.

 // SASS loader
 // https://medium.com/@Connorelsea/using-sass-with-create-react-app-7125d6913760
 {
     test: /\.scss$/,
     include: paths.appSrc,
     use: [
         {
             loader: 'style-loader',
         },
         {
             loader: 'css-loader?modules&importLoaders=1&localIdentName=[name]__[local]___[hash:base64:5]',
         },
         {
             loader: 'sass-loader',
         },
         {
             loader: require.resolve('postcss-loader'),
             options: {
                 // Necessary for external CSS imports to work
                 // https://github.com/facebookincubator/create-react-app/issues/2677
                 ident: 'postcss',
                 plugins: () => [
                     require('postcss-flexbugs-fixes'),
                     autoprefixer({
                         browsers: [
                             '>1%',
                             'last 4 versions',
                             'Firefox ESR',
                             'not ie < 9', // React doesn't support IE8 anyway
                         ],
                         flexbox: 'no-2009',
                     }),
                 ],
             },
         }
     ]
 },
 {
     test: /(\.bootstrap\.css$|bootstrap-theme.css|bootstrap.css)/,
     use: [
         {
             loader: 'style-loader',
         },
         {
             loader: 'css-loader',
             options: {
                 minimize: true || {/* CSSNano Options */}
             }
         },
     ],
 },
 {
     test: /^((?!\.bootstrap|bootstrap-theme).)*\.css$/,
     use: [
         {
             loader: 'style-loader',
         },
         {
             loader: 'css-loader?modules&importLoaders=1&localIdentName=[name]__[local]___[hash:base64:5]',
         },
         {
             loader: require.resolve('postcss-loader'),
             options: {
                 // Necessary for external CSS imports to work
                 // https://github.com/facebookincubator/create-react-app/issues/2677
                 ident: 'postcss',
                 plugins: () => [
                     require('postcss-flexbugs-fixes'),
                     autoprefixer({
                         browsers: [
                             '>1%',
                             'last 4 versions',
                             'Firefox ESR',
                             'not ie < 9', // React doesn't support IE8 anyway
                         ],
                         flexbox: 'no-2009',
                     }),
                 ],
             },
         }
     ]
 },