If I get it right from reading https://github.com/ncw/rclone/issues/2903, rclone does not support checksum for crypt remotes. I get this feeling from reading the help text suggestion of the OP:
-c, --checksum Skip based on checksum & size, not mod-time & size. If checksums don't exist(crypt), then just size.
At first thought it makes sense. After all, the check sum computed by the remote would be completely different than the local checksum. Its encrypted after all.
But after a second thought: why don’t we encrypt the files locally for the only purpose of computing a check sum, and compare this to the remote checksum?
Would this work? Am I missing something?