Hello, I just figured it out thanks to you pointing out the S3-no flags. This command works:
rclone copy backup.zip s3-backup:node-backup/at-vie3 --s3-no-check-bucket --s3-no-head --s3-no-head-object --s3-no-system-metadata
I had to add --s3-no-head --s3-no-head-object.
I somehow completely missed these. Thank you for letting me know! And sorry for wasting your time. Hopefully, other users will be able to find it