Wiki navigation is not content, though. That's a significant difference. It's also consistent, community-wide.
While it is true that most links in the navbox would be available by drilling down (and/or up) the category tree of one of the categories the article belongs to, it should also be true that any article/category link available in MediaWiki:Wiki-navigation is presumably available by drilling down from Category:Browse and arguably should also be linked to from the main page.
I don't dispute the first part of that (category drill-down), and that's the premise of Mobile Main Page. The second part is a little fuzzier. Wiki-wide navigation drilldown should also, in theory, from Category:Browse; in practice, not all wikis do this (or use Category:Browse at all). Further, drill-down to any given page is not how most readers navigate in the first place. The most common behavior (by far) is search.
I don't disagree at all with you about surfacing contextually relevant links. I'm disagreeing that navboxes are the obvious solution. In addition to being a difficult pattern on mobile devices, the usability testing shows that they come off as more noise than signal beyond a few links. And that makes sense, for the same reason that restaurants break up menus into groups of no more than a few items (and add more data to those items to describe them). By that rationale, it's really not about having the cluster of links at all: it's about showing enough relevant context for why a reader should follow those links. Quality and context trump quantity. Having a list of links without context is noisy.
So, I'm not so much making an argument for "naviboxes" specifically, but I think "footer navigation that can be contextually customized/specified per article" would be something that is great to have even for mercury. MediaWiki:Wiki-navigation is a list that is up to three layers deep. Most typical naviboxes are also three-layer-deep lists (header being the first item of the list). Thus conceptually we could have a "article-specific footer navigation system" that is specified as wikilists much like MediaWiki:Wiki-navigation, and mercury can turn it into a footer menu while desktop skins displays it as a navibox.
While -- once again -- I'm not disagreeing with you on principle, testing shows that people just don't use the footer for that on mobile. Adding three-layer-deep lists to an already minimalist-interface is just too many taps; users won't traverse it. They might do one tap per page to get to other pages, but digging / drilling down is too much work.