It looks like plenty of additional adjustments would need to be made.
One thought is each location in the table of contents would have two parts:
- a container page with the header and content added by inclusion wiki effect,
- text content page.
However, this may complicate matters for editors.. but perhaps not. As it is right now, any new handbook page must have the proper navheader included, as well as an entry in the table of contents page. Instead of those two steps, perhaps just a category tag that would mean "add to handbook" which is a simple thing to do: [[category:handbook]], and a reasonable thing to add for all handbook pages.
The wiki inclusion effect is transparent to everything else, but as you can see by the current state of this page (Flat html) there are multiple instances of the headers and the required TOC makes things additionally messy.