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Instead of creating a migration strategy guide in the release docs, I went the route of detecting when a v3 container was being started with a v2 file structure, and then auto-migrate the file structures for them during container initialization.
This would potentially be a breaking release, in the event that two octoprint containers are using the same volume and the second container is added while the first (which is a v2 container) is running.
However, I've decided against classifying this as a breaking change (and thereby requiring a v4 release), because the current design of octoprint and octoprint in docker does not really support horizontal scaling due to the requirements to bind a host device.