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You're correct that the PAT interface only downloads datapoints within the UI, which is intentionally capped to limit bandwidth. The server UI doesn't currently have a "download all" functionality for much the same reason - bandwidth management. The OpenStudio Server API contains the download functionality. Here's some Ruby code that may be close to what you're after.

The limit in PAT isn't hard to change, and could probably be turned into a preference value. Similarly a download all button could probably be added to the server interface without much trouble. This is the sort of thing that would be good to post on UserVoice to let the community weigh in on preferences.