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That's correct, at present the Project level custom data is envisioned primarily as a place for script writers and the like to persist data, though your use case sounds quite compelling.

Custom data on tasks and resources can also be added to HTML reports by customizing the template. See the help entry "Customizing HTML templates". Would you find it useful to be able to do the same with project custom data, or do you have in mind to add the project version to the header or footer of each printed page?