Currently FreeNAS GUI does not support setting rclone command line options. I needed to limit sync speed, therefore need to modify the –bwlimit parameter. I will show you how you can do that in current version FreeNAS 11.2-U7

Edit the following file

/usr/local/lib/python3.6/site-packages/middlewared/plugins/cloud_sync.py

around line 106 and add bwlimit, example:

        args = [
            "/usr/local/bin/rclone",
            "--config", config.config_path,
            "-v",
            "--stats", "1s",
            "--bwlimit", "25M",

Then restart middlewared:

service middlewared restart

Start the job

Now start your cloud sync job and check that the rclone process is using bwlimit or any other parameter you specified:

ps aux|grep 'rclone'

Note: this will probably only work until you apply the next FreeNAS update.