ZIP files can have block-like relatives to the SQLite page. It could still be a single XML file and have piecewise encryption in a way that change saving doesn't require an entire file rewrite, just the blocks that changed and the updated "File Directory" at the end of the ZIP file.

Though there would be opportunity to use more of the ZIP "folder structure" especially for binary attachments and icons, it wouldn't necessarily be "required", especially not for a first pass.

(That said there are security benefits to whole file encryption over piecewise encryption and it should probably be an option whether or not you want in-place saves with piecewise encryption or whole file replacement with whole file encryption.)