Yeah the list tool is more just meant for making enumerated or bullet lists, not actual outlining.
For that, Scrivener is designed to handle the outline to whatever depth (and width) you need it. Take a look at the Scapple or Scrivener outlines on our support page for one practical example of this. While it is true that much of the outline you’ll see in these projects is directly related to the sectional structure of the manual, there are also many sections that do not follow the rules. For example in the menu system appendix of the Scapple manual, you’ll find each menu command has its own outline node. When menus get reorganised, I just have to drag commands around instead of copying and pasting between menu files. Yet, when you look at the PDF it will appear as those these are all on the same “page”.
The tool used here is the “Compile As-Is” flag (which has some important other effects, but one effect of it is that they won’t print their titles if they otherwise would have, effectively hiding the fact that they are outlined, from the output).
This is just one of many tools in Scrivener for tuning how the visible outline in the Binder gets converted into a reader-use topical structure; including ways to cause the outline to vanish on output, in a sliding scale all the way down to there being no apparent connection between the main outline and the output. The scale goes from having Scrivener handle more of the structure for you, and having to be more literal with your outline, down to handling more of the structure yourself and being more free with the outline. An example of this give-and take: you can disable the feature that separates text files with an empty line or other separator. If you never outline lower than the scene level, that’s a useful feature, but if you want to break a scene down into even smaller sections, you don’t want “scene breaks” in between those sections. Now you’re responsible for handling the scene breaks (what I do is just make a special file that is nothing but the scene separator, called “——-” so that I can use it like a visual divider).
Another approach, rather than breaking the actual pieces of the scene into separate text chunks, is to maintain a conceptual outline for that scene that you do not really use as “files” but just an outline. It’s actually very easy to work that way given how Scrivener is designed. You can build out outlines beneath text files just as easily as you can with folders. Try loading up a scene, and then hit Cmd-3 to enable Outliner view. You’re now looking at the contents of the scene (probably empty). Start outlining here. Hit Enter to make a new entry, Cmd-Ctrl-ArrowKeys to move items around and indent them, and when you’re done just hit Cmd-3 to toggle back to where you were in the text. You can flip back and forth between the text and the conceptual outline fluidly. You can greatly simplify the Outliner too by removing columns. For concept outlining, I like even the icons turned off; nothing but titles.
This approach can be made to work seamlessly on export, by telling the Compiler to disregard all outline items beneath a certain depth. You are then free to use that “floor” to be as prolific as you want with notes and outlines stored “beneath” the scene files.
Another tactic is to reserve one of the container types (folder or file stack) as “invisible”. Turn off all outputs for it in the Formatting pane, and now it can be used as an invisible grouping mechanism that only you see.
I guess the short version is: don’t confuse Scrivener’s capabilities with anything you see in a template. The templates assume and demonstrate one (common) way of working, but by no means are meant to define the limits of how the program can be used. In the end, you are working with a freeform outliner that is coupled with an export system that works a bit like styles, where you can tell the exporter to do certain things (or nothing at all) with the outline’s content, both its text and title, as well most other data about it, such as the synopsis and document notes. There is a ton of flexibility there. Fundamentally there is no “chapter” object in Scrivener. We make up what “chapter” means by type (and sometimes position), only when compiling.
What that should mean for you, ultimately, is that you can use the outliner however works best for you. In most cases you can make the compiler work with what you’ve got. Finding that point will likely take some time acclimatising to the software, learning what it is capable of, and learning how the compiler uses the Draft outline to produce a document in the end.
Just remember you’ve got group, split and merge commands in the Documents menu to help you out with all of this.