It seems the navigation/TOC panel is closed by default, and there is no way to save it with it open.
Much functionality is lost or obscured in DC from what I've seen, if this is gone it's a big loss. I want to deliver better docs, but our users don't even know PDFs can do this so they will not do the steps required to open that panel.
Truly hope there is some workaround for this, please advise.
doh, soon as I asked the question I found a way to do it - yeah!
File > Properties > Initial View
I was nearly sure this worked just to save but at least it can be done.