--checksum is probably going to help the most.
You could try increasing this too 1,000 is the max AWS support but I know Ceph supports larger and minio may too.
--s3-list-chunk int Size of listing chunk (response list for each ListObject S3 request). (default 1000)
So the names don't have / in them 
You can potentially do a sort of manual sync like this.
rclone lsf -R source:bucket | sort > source-sorted
rclone lsf -R dest:bucket | sort > dest-sorted
comm -23 source-sorted dest-sorted > to-transfer
comm -12 source-sorted dest-sorted > to-delete
rclone copy --files-from to-transfer --no-traverse source:bucket dest:bucket
rclone delete --files-from to-delete --no-traverse dest:bucket
It would be interesting to find out how fast the first rclone lsf -R is on your 10M file bucket.