Let's open this topic with a comment designed to split the readers into two camps.
Don't fall into extensive reordering the e-book spine trap. It has no real benefits, raises the cost of production, and reduces and devalues "The Book".
- Remove the minimum number of pages you can. That probably means Half-title page.
- All sections don't have to be in the NCX, and they don't have to appear in the NCX in the order they are in the spine. (Explained later).
- e-Up the various front and back matter section concepts rather than destroy them as irrelevant for e-books.