Good catch -- you are right, -R is important!
Yes and no... with rclone check it is possible as you can just switch the src and dst args, but with rclone checksum the sumfile is always the src, so it's not really possible to go the other direction. That would be another good feature request -- I don't think it would be too hard to implement this.
That said, I think it is already the direction you would want. You aren't interested in files that aren't in your sumfile, right?
One other thought is to use --missing-on-dst / --missing-on-src and just discard whichever one you don't want.
Ok, I think I understand what you're getting at now. The --files-from method is probably the best option for now, and a feature request for a better one would be helpful.
Note also that if bit rot is your main concern, using --download can be a more foolproof method than checking stored hashes, as some platforms simply return whatever hash was stored at the time of upload (i.e. they won't necessarily catch bit rot that happened later.) There's an interesting discussion about that here and here.