Hi Thomas,
Sorry for the confusion. Our purpose is moving all extensions' menus into one place ("Meta Box" top-level menu). That keeps everything organized and easy to find.
The reason we named the menu "Custom Fields" is Meta Box Builder is for custom fields only. There are also other extensions that for custom post types and custom taxonomies. When they are activated, you'll see full menu like this:
https://i.imgur.com/EHd1v23.png
This post explains the idea of shared menu.
And when we refer to custom fields, naming field groups make sense, since they're a group of fields. It's not groups in Meta Box Group. It simply means a set of custom fields.
I'll update the documentation to make it less confusing.
Thanks a lot for your feedback.