By a conventional reading of http://www.tei-c.org/release/doc/tei-p5-doc/en/html/index.html , the Back Matter Comes before the Text Body, which seems a little odd.
this seems like a non-issue to me. the design was come up after long discussions,
and presents the contents in the way that was deemed most useful. It is not supposed to be a conventional reading.
We had a long process of consulting among Council and then with the community before finalizing on this layout. Please check the previous discussions on TEI-Council and on the ticket to see the reasoning behind it. The main idea is that what people want to click on most is most accessible, and is visible, while the main TOC takes centre-stage.