iCloud comprises several components. One of them is the file service with iCloud Drive being its user-facing part. Another component is CloudKit, a database service that works behind the curtain and can only be used by applications directly.
DEVONthink’s old iCloud sync was based on the file service which did not let it live up to the maximum possible performance. Contrary to that, the CloudKit sync uses the backend database’s capabilities for a fast, single-pass sync.