My final solution is not perfect but works for me.
Maybe somebody else finds it helpful.
If you only need to generate (simple) directory (file) listings (e.g. by cmd: rclone lsjson...) which you want to import into SQL by php-script and invoked or accessed via a browser... and you also face permission or security issues you could do the following:
- let the php script generate a log or tmp file as the "trigger"
- execute the needed rclone command - triggered by incron or similar additional software (http://inotify.aiken.cz/?section=incron&page=why&lang=en) - can be installed by apt-get under Ubuntu