After making a few changes, I think the actual issue is instrumentation- a false alarm. htop shows those multiple instances, but top only shows one.
I’ve also switched away from using crontab to call the script. Instead, I’m using tmux and launching each shell script in it’s own tmux session, so that I can connect to each one individually and watch the current progress with rclone -P. This is a much simpler solution, and my memory usage has dropped significantly by changing --checkers 2 --transfers 2 to --checkers 1 --transfers 1 and by adding the --use-mmap flag. Thank you.