So, turns out the documentation might not be correct for this aspect. The manifest.json needs also an adjustment at a different level to visualize the style in the builder.
We needed to D:\App\ArcGIS\Portal\apps\webappbuilder\stemapp\themes\themes-manifest-builder.json
If you want to make the app refelct the changes also in the viewer context, you need to mirror changes in the WebAppViewer folder in \ArcGIS\Portal\apps ...
It's a bit more complicated compared to the dev edition but it is manageable.