I did understand your original request. The last one, of embedding the text into a meta-data field so you can use a token to place it later on, disregarded that of course—but I totally understand where you are going with this thought, and have worked with outlines that either support the notion or depend upon it heavily. LEO is probably the best example of an injection based outliner—it’s kind of like Scrivener for programmers. It takes your source code and turns it into an outline so you can visualise your project’s code method by method as tree nodes. It can be very injection based, with meta-nodes that simply list inclusion nodes, or common header nodes and etc, but the base nodes are always visible in the outline, even if they are only meant to ever be included indirectly by other nodes. It’s a great system, and you’ll never hear me saying it isn’t.
My primary point in the first paragraph is that I’m not sure it is the best system for Scrivener. For code, this makes sense not because it lets you place tree-section G in the middle of tree-node-Y, but because the duplication of key texts is a common task. Injection is incredibly useful when you have “Header-plain Header-code Code Footer” structures. A lot of that is going to be the same in every single file, so why not declare it once and inject it a thousand times instead of pasting it a thousand times? But a book is nothing like that, and a book is what Scrivener is all about.
So that leaves one-time injection, and that is less useful for reasons which you actually went into later on: Scrivener’s outline is powerful because it lets you actually fathom and manipulate the structure of your book just as easily as the text of your book. If you start obscuring the structure into the text, that relationship between the two degrades. There are very few advantages to injection over smaller nodes, in a one-time scenario—especially when there is nothing about the software that punishes you for small nodes.
Consider your own example: you have a scene with a smaller sub-scene (flashback, whatever) in it. The Scrivener method would have you split that into three pieces. What I would do, to logically contain it, is create an empty scene file and then put these three components into it—that way they are set apart from the other scenes around them and it is clear they are meant to be one scene. It presents one single target to click on if you want to view that scene from a macro point of view (using Scrivenings), in the same way you would view any scene around it that is contained in one file. It can effectively be treated as one file until you disclose the group and examine its parts. That’s a big concept in Scrivener and it should be used liberally when necessary. This is, in effect, what you want: a way to hide the fact that scene 48 has a flashback in it, because in a list of scenes in that chapter, unless you disclose the scene container, it will just be another scene in the list—but if you need to know where the flashback is, this method makes it easy to find it and view it with all of Scrivener’s modelling capabilities! That’s something an injection code couldn’t provide.
You might not always need that full power, but it’s there if you do—you don’t have to prepare for it or anticipate it. If you work in small nodes, then you are already set up for powerful derivative cross-analysis. If you’ve peppered a bunch of injection codes and then later realise you’d really like to view a collection of all the flashbacks to make sure the continuity is correct—well you can’t—then you’d be back here for another request support asking to allow collections of injection markers. 
What if you decided you want to take that sub-scene and append it to the larger chunk of text it came from. You’ve read through the proof, and this section feels to jerky with the small sub-scene in it. So in Scrivener you just grab the red label file and drop it in front of the red label scene it corresponds to. You’re done—the original scene is now a seamless whole. You could merge them together if you want—but you don’t have to—I don’t. I keep spits forever because I like to see where I’ve fractured the book before. As you can see, making this edit with injection codes would actually involve a couple moves, not just one.
I think you get what I’m driving at here. The outline is much, much more than just Composition 101 stuff. It’s a macro-image of your book’s skeleton in a way that an external pre-thought outline can never be. It’s an amazingly accurate topology, if used liberally in this fashion. It could just be an artifice—a “Chapter 10” text file that is 8,000 words long and nearly as unwieldy as it was in Word, but it needn’t be if one wants.
Injection would cripple this because suddenly structure would be a property of the text, which is a thing you cannot see in a stack of index cards or an outliner tree. You are back to the word processor problem that most of us fled from.
You raise a point on how it is easier to move an injection point than a node through text itself. On the surface this seems true. If you want to move the flashback three paragraphs up, you can’t just move the flashback node up. However on second examination it’s actually no more difficult in Scrivener than in a free-flowing text example. Just click on the entire scene as a node, and in Scrivenings edit the position of your flashback node by moving text around it; an opposing gesture to moving the injection mode around the text, but ultimately no different. Since you can edit the textual topology of a list of nodes just as easily as you would edit text within a single node, many of the limitations and obstructions in the node system vanish. Or to put it another way, other outlining solutions have developed injection code as a simple substitute for what Scrivener is doing. The ability to edit the textual topology in an amongst the outline topology, or working completely upside down from an outliner point of view, means you can treat your text (with a few exceptions) as “simply” as you would in a word processor, without losing the benefit of a solid outline methodology.
I think this is a slightly askew way of looking at things. It is not as though the parent implicitly includes its children. In fact you can exclude the parent from compilation entirely, and its children will still be included. Compile ignores and uses depth in different places, and this can make things confusing, but you could think of it this way:
- When it comes to constructing the text of the book, it approaches your outline as a flat, linear list from A to Z. If an item is excluded, it skips to the next with complete disregard for the relationship between the items before and after the current item.
- When it comes to “formatting” the text, it pays avid attention to depth, context, and node type. Full control of this is in the Formatting pane, where you can describe rules for document type and depth.
Where I’m not sure I follow your argument is when you state that this above treatment of an outline makes it difficult or impossible to construct an outline tree of arbitrary depth. I would say the complete opposite. The fact that the tree is treated as flat no matter how deep it goes in fact enables the tree to transcend mere book structure and become a true author’s tool. That you can break down a scene into sub-pieces and have that break-down be completely invisible when compiling means the outline is no longer just for the reader’s indirect benefit via the delivery of strict depth-based titling. So I might not be understanding what you are driving at here.
Now, you do have a point in that injection allows non-linear “cloud publishing”. I suppose that term has been thoroughly soiled by the buzzword brigades these days. I don’t mean using the Internet to publish: I mean publishing a thought cloud rather than a linear “this is the book” construct. Yeah, Scrivener’s not really set up for this wiki-like approach, and I submit that altering it to do so would cripple some of its utterly unique powers—for a technique that most people would never use. Honestly, many people never get past the “list of chapter files in the Draft folder” technique. Yeah, they are missing a huge amount of Scrivener’s potential, but cracking a book down into a thousand pieces instead of 20 pieces is a huge cognitive leap that may not even be necessary (and certainly isn’t superior) for most people, many of whom started out on a typewriter which is about as linear as you can get.