The Novel template is already set up to work in an alternate fashion if one does not wish to outline down to the level of scenes. The “default” workflow as described is what you quoted, but if you search the template instructions for “Working with chapters instead of scenes”, you’ll find instructions for using files as chapters instead of folders with multiple many files.
Really you only need to worry about steps one through three while writing, but you’ll want to set aside the rest of these notes when it comes time to compile as there will be a few tweaks you need to make (and hopefully in doing so you’ll see how the relationship between the Binder and Compiler is very flexible, and that what you see described in the template is only one possible way of using Scrivener—quite likely not the best way for you, at least with this project).
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Regarding numbering, I’m not sure if it has been said here, but there is a way to number index cards, using the View/Corkboard Options/Show Card Numbers. As you’ll probably be working with a flat list of text files in your Draft, this may work well for what you need.
I believe some extension to this in the Outliner is on the slate for the future (I’m not sure of the status at the moment; I do know it was under consideration), but if any kind of numbering were to be added beyond what you see here in the Corkboard, it would stop at the Outliner and not continue on into the Binder, where space is at a premium and the visual design has always focussed on keeping things as clean as possible (we get all kinds of requests for this feature or that feature to be added to the Binder—it would just end up being the Outliner if we added them all, and there already is an Outliner that does everything most people ask for).
One problem with the notion in general is that Scrivener is too flexible for something like true print-accurate numbering to be easily implemented. Consider for example, those who like to keep writing notes directly alongside the manuscript, by disabling the “Include in Compile” checkbox in the Inspector. Such files will not print when you compile. Should they be numbered? Probably not, but not everyone uses that feature the way I just described it—some use it to temporarily exclude portions of the manuscript so they can proof three or so chapters, in that case the excluded stuff probably should be numbered—-and that is just one potential complication with one feature.
Considering that, and the fact that most all of the reasons one would need print-accurate numbers with a word processor + plethora-of-external-tools-both-digital-and-analogue are solved by Scrivener’s design of folding the external organisation directly into the manuscript. When you can drop a link to a section from another section (including the global Project Notes), isolate a plot thread with a single click or have your cross-references numbered correctly on compile, there aren’t many reasons left for needing numbers. Collaboration, as you point out, is probably the largest reason left, for those that cannot all be using Scrivener to work on the book.
Hence, there is nothing more complicated than simple card numbering that isn’t even print-accurate in all but the most basic scenarios.