The difference is Package Groups vs Package Option Groups. The video CubicWebs linked is a good one to watch for a basic understanding of Package Options.
Package Groups contain 1 or more Packages
Package Option Groups contain 1 or more Options
On order forms, Package Groups are displayed like categories, with their member packages within them.
When configuring a package to order during check out, package options will be requested, and ordered similarly within their package option groups.
I hope this makes sense, and thanks for bearing with us. Our documentation can definitely use some help, we're updating it as we can and hope to be caught up soon.