The developer of Scapple (who is yes, the same person that makes Scrivener) not only agrees with what I said, but was the person who originally said these things, and specifically designed the program to be flat—we even went out of the way to avoid features that might look like hierarchy, so that it wouldn’t be confusing—shapes were the big compromise in that, but only from a UI standpoint.
If you don’t believe me, open up the .scap file in a plain-text editor. You’ll see each note is in a flat list, there is zero hierarchy in the Scapple format. Worse, connections are just references to other notes from the originating note. A note can have zero, one or five-hundred link references. You cannot have hierarchy in a purely equal system like this, where any note can link to any other note no matter the conditions of that note. Even background shapes, which I mentioned before, are not an example of hierarchy. There is a separate list of shapes below the notes list, and you will find no association with “its” notes, in this file. The only thing that “associates” a note with a shape is if it happens to overlapping it—and a note can be overlapping two or more shapes to create a fuzzy declaration (meaning that on export, some data in the form of associative declarations like this will be lost, since a hierarchy can only represent one parent per item).
You had me up until the tree bit. Scapple can be used to create networks, this is true, but this is of course a very broad word. A network can even be anarchic in its component parts (which I would say Scapple is probably a good example of). To then suddenly leap to thoughts of hierarchy trees is to focus on only one single (albeit popular and familiar) approach to the concept of associating thoughts together. If you want to look up something that is closer to Scapple’s approach, do some research on concept mapping. It’s not quite the same, mainly in that it relies upon an explicit declaration for each connection “is a”, “will be”, etc., but it also uses a flat non-hierarchical approach to thinking. Connections are not declarations of topical lineage, but of association.
Only if you insist on using Scapple like a mind-mapping program or a visual outliner. It’s not designed to be used that way, however. You would run into as many problems trying to use it like Powerpoint. It’s meant to be purely flat, no disclosure, no parental assignments, and thus: no restrictions on how you form connections, no requirements to chain an idea to another idea, and no stigma to bind oneself to the principle of categorisation for everything they do. Whether that’s your cup of tea or not is up to you, but I’m just telling you what the program was designed for and what the people who enjoy using it like about it (and wouldn’t want it to radically change, turning into Yet Another Outline Based Mind-Mapping program).
So yup, Scrivener is a tree, and Scapple is a map. They are oil and water, and that’s precisely the point: Scapple is for the types of thinking that are abstract. Scrivener is for the types of thinking that require structure and rigidity. The two can be a part of the same project in different phases, but the two are meant to be discrete, performing for different cognitive outlets. There are some basic copy-and-paste type procedures that can get data between the programs—but they are lossy, always will be, and are meant more for transition than integration.