" Encapsulation is effectively a natural property of having multiple trees."

I pondered the first part of this document for a long while: "tree of trees" makes no sense. Graphically, a tree of trees is just a tree. Look at all the diagrams in the first part of the doc: just trees with solid or dotted lines and some superfluous-looking boxes.

Eventually it came to me: 'tree of trees' was invented to explain that parts of the tree are encapsulated from other parts.  Eventually this was confirmed in the quote above.

The story would be much clearer if you say that right when you introduce the neology 'tree of trees'.  Rather than starting with complicated definitions, just say that the Shadow DOM spec defines new encapsulated DOM sub-trees. When we introduce this encapsulated sub-tree into the existing DOM tree, we call the result a 'tree of trees' to emphasis the encapsulation while also showing that tree navigation operation existed between pre-shadow-DOM nodes and Shadow DOM nodes.