Not to drag this thread out, since I have a workable solution, but I am curious: is that something that makes sense as a feature for rclone? ie. allow --checksum to be used with crypt and encrypted remotes.
It would be a great addition in my case, but I obviously don't know everything that would go along with creating something like that.
Edit: looks like this has been discussed here: Make --checksum work with crypt remotes
And I think there's an open issue on Github here: https://github.com/rclone/rclone/issues/1712