[6.6.0RC4 - nginx upstream timed errors]

Oh it won't affect performance at all - as soon as the command is entered the original binary handles everything so you won't gain anything by running it "directly" . If you check your running processes you'll already see rcloneorig and not rclone even though you invoked rclone.

[6.6.0RC4 - nginx upstream timed errors]

@DZMM
'rcloneorig' is in fact the true rclone binary. When invoking 'rclone' (when using my plugin) you actually invoke a wrapper script that calls rcloneorig and injects the config path just as the example i posted above.
This is done so the config can be kept on the flash drive as to keep it persistent across reboots, but to keep the command consistent with what it would be on other systems.  

[6.6.0RC4 - nginx upstream timed errors]

@DZMM
Considering this only happens when you actually run a rclone command i don't think it's related to the plugin but perhaps more likely the rclone command itself.

If somehow the wrapper is causing the problem you would be able to solve it by invoking:

rcloneorig --config /boot/config/plugins/rclone-beta/.rclone.conf move /mnt/user/rclone_upload/google_vfs/ gdrive_media_vfs: -vv --drive-chunk-size 512M --checkers 3 --fast-list --transfers 2 --exclude .unionfs/** --exclude *fuse_hidden* --exclude *_HIDDEN --exclude .recycle** --exclude *.backup~* --exclude *.partial~* --bwlimit 9500k --tpslimit 4

This bypasses anything the wrapper is doing to the command. I would be surprised if this was the culprit though.