I believe this is in fact because of the behaviour of the Boost Theme.
I tested it on a MoodleCloud site with Boost set as default Theme.
In fact I think the items you are seeing on the "right" are just navigation.
The Table of Contents is actually in a Block below the Book content - see screenshot below.
While this might make sense with some types of resources and activities, because the Book TOC is 'naturally' next to the content, it definitely feels strange have this TOC now below the content