What Scrivener does that nothing else does as well
It is worth saying this first, because a comparison that pretends the other tool is bad is not a comparison. Scrivener has been the serious novelist's manuscript organizer for close to 20 years, and the reason is the Binder: a book as a tree of documents you can reorder by dragging, with a Corkboard and an Outliner reading from the same structure. Nothing about that model has aged. Calamus is built in the same tradition rather than against it, and a Scrivener user will find the Binder, Outliner and Corkboard sitting where they expect them.
Scrivener is also genuinely deep in ways a newer tool is not. Its compile system is scriptable to a degree Calamus does not attempt, its scrivenings mode for editing several documents as one continuous text is excellent, and its snapshots predate almost everyone. If what you want is a manuscript organizer and you are happy finishing the book somewhere else, Scrivener at $59.99 is a reasonable answer and has been for years.