First of all, I have to say that I feel like, while the list used by Qubes on their documentation would be detrimental for something like a Quick-Start-Guide, I also feel that it does make at least some sense and serves a purpose when it comes to a "real/complete/long" documentation. It gives you the ability to quickly scan over every available article, to find what you need. It isn't that pretty and shouldn't be the default/first thing a user sees, but as an optional addition to make a wiki more accessible, gets the job done. What we actually use as the front page for our documentation currently (https://www.whonix.org/wiki/Documentation), should probably not be the first thing a newcomer sees/reads, but shouldn't be removed for that reason alone.
Now, the Mozilla approach is interesting. Just like myself, with the Quick-Start-Guide, they move the bar with the main topic below the text, when in "mobile mode". Works and preserves screen-estate.
The implementation Elementary used looks good as well. Making subtopics in a site "clickable" to link to them directly is a nice way of keeping a long page manageable. A combination, like you suggest would definitely have benefits. Making "Isolation", "Safety", etc on the first page, for example, clickable makes the whole thing appear more rounded.
I can agree that "hamburger menus" should be avoided, as they'd just make looking for a certain topic even more tedious, than such a task already is.
Now, I'd love using a side-bar like "zurb", blending in and out once someone hovers over it with a curser. This though seems to be only possible with JS, according to my research. Now, as for making the current page highlighted, that will be implemented by me. Shouldn't be to hard. Either by changing the color of the current topic or using pictures instead of text. Should have gotten that idea myself...
Have a nice day,