I'd be more inclined to author each article as a single index.html page in its own folder. Any CSS, images, js, etc. that the page calls would also be in that one folder. Then package the folder and use this as your article content.
This way, you'd have automatic swipe navigation to the previous/next article, DPS will preload neighboring articles to speed up the load experience, and each article could be in the collection browse page.
How is your HTML set up? One tall HTML or separate HTML pages? If one tall HTML, how about links to anchors in the HTML? If separate, aren't you able to use the same navto:// link structure? I thought you could but I could be wrong.