Ah, but they are! And that’s essentially what’s creating the problem.
First, the thing that makes Scrivener projects so special, that makes it possible to have loads of research material and several hundred of thousands of words in the manuscript and not make the computer slow down, is that every sub-document you have in the binder is stored as its own file on the hard drive. A Scrivener project isn’t a file, although it looks like that on a Mac. It’s a folder with perhaps thousands of files inside it.
When you are working on a project, Scrivener only opens the files you have visible in the Editor. One advantage of this is that if something happens to your computer while you are writing, only the document/file you have open in the Editor is affected. This makes Scrivener’s file system very robust.
Secondly, when you have your projects saved on Dropbox, they are not. They are saved on your Mac, in a folder called Dropbox. The only special thing with this folder is that the Dropbox app you have running on your Mac is always watching that folder and uploading any changed files to the Dropbox server, and also watching the Dropbox server to see if any files over there has changed and if so download them to the Dropbox folder on your Mac.
If you have the project open on two Macs at the same time, you could easily end up in a situation where both Macs try to read and write the same document (file) in your project. The Dropbox app on either Mac doesn’t know this. It only compares the files in its own Dropbox folder on its own Mac with the files on the Dropbox server. If it thinks that the version on the Dropbox server is newer, it will download it to its Mac and overwrite the document/file you have there.
In the worst scenario, what you are writing in a specific document on your Mac would suddenly disappear, because something happened on the other Mac, telling the Dropbox server that its version of the document is the newest, and the Dropbox app on your Mac simply getting that info and thus downloading that version from the Dropbox server.
Everything IS automatic, but computers aren’t very intelligent, so if three computers are simultaneously accessing your project (your two Macs and the Dropbox server), there will be trouble sooner or later.
Always close the project when you are not working on it, and always wait for the Dropbox app to upload any changes before closing the Mac.