The gist is the by line or second heading that an author has on the title of a book.

For example the book Natural Brilliance ... that's the title
Underneath is written "overcome any challenge... at will" That's the gist.

Since syntopic reading involves 4 or more books the central purpose is what you want to understand about the book. Themes are the main points the author is covering. Explained at item 7 for the steps of creating a syntopic mind map. They are not branches. On the branches you write the relevant passages from each book that addresses your purpose and what you wanted to learn from the authors.

Alex