The Scrivener file format isn’t a proprietary format, though. It’s a basic package file. It’s just that Scrivener is overriding some of the default behaviors (so the entire package doesn’t have to be saved/read, just the changed documents in the package) and iCloud sync doesn’t provide corresponding mechanisms for incrementally syncing package files (if I’m understanding it correctly).
Here’s more detail:
Very, very quickly (because I’m snowed): iCloud has no problems syncing a folder or a package file or anything else. That’s not exactly the problem. There are generally two types of app: shoebox apps such as Photos and iTunes (and Ulysses, for that matter) which have a single window that manages a single database of files, and document-based apps, which use a different window for each file, and whose files may be anywhere on your computer. Shoebox apps provide a window on a large amount…