Thanks for clarifying. Information on the rest is sort of scattered around and high level compared to the Cryptomator “Security Architecture” article, which concentrates on single focus and so can get deeper.
The backup process explained in the manual tries to show things in simplified terms. For technical, see
How the backup process works and How the restore process works, but encryption is just a minor part.
Block-based storage engine starts at high level concepts, then links to a (2014 - so dated) detailed PDF.
The Developer category you are in has other specific topics like on the channel pipeline, file formats, etc