Mounting the folders worked great, once I found a proper dedupe tool to run locally on my machine. There are a LOT of bad ones out there but I can recommend czkawka based stuff at least.
Deleting files from the mounted drive is much much much slower than rclone delete, it’ll take hours not minutes. I wonder if this is because I chose –network-mode or is it always like this for large changes to an rclone mount?