Can you mount these both as file systems? I think you must be able to if you are using rsync on them.
It can as it has a lot more parallelism - you can increase --checkers and --transfers to check many directories at once and transfer many files at once.
rclone doesn't do the differential sync that rsync does - it transfers whole files only, but I don't think you really need that with millions of small files.
The "checkers" function are identify the modified files on source (update/new/delete) and copy they directly to target or put they in a queue to be copied by the "transfers" ?
Do you know the percentage of resource consume for each checker and transfer about cpu, memory and IO ? (the question is to understand the impact on source)