I got it working doing the following:
- download github repository: https://github.com/concrete5/concrete5
- copy concrete/themes/atomik folder to application/themes and make necessary folder, file and class renamings (check the @afixia guide)
- make another ‘build’ folder in application/themes
- move concrete/themes/atomik/main.js file to build/assets/js
- move concrete/themes/atomik/css/scss folder to build/assets
- copy concrete/themes/atomik/css/presets/default folder to build/assets/scss/presets
- delete main.js file and css folder from atomik
- follow steps to compile js and css from the new guide:
- npm install
- npm i @concretecms/bedrock
- npm i laravel-mix
- npm run production
Then make any style changes in the build/assets/scss files and recompile.
That’s it. Seems to be working so far… 
One minor thing though - if I put my build folder somewhere else on the computer and use a direct path to the theme in the webpack.mix.js, the main.js file gets copied together and inside all those path folders, not just itself.