and the files you are upload aren't appearing in the rclone mount?
no remote files should be going there - it's only used for the script checker files, so I've no idea how you managed that. Maybe when you were trying to setup you did something odd??
My advice is to unmount everything, delete /appdata/other/rclone, delete any residual files and folders out of /mnt/user/mount_rclone and /mnt/user/mount_mergerfs and start with a fresh run. Lots of people have problems initially when they don't set it up right. I think you know what you are doing now, so a clean start is probably best.