What is the right direction to go in and ill explore, just not sure how to communicate with gateway and assume all the tor stuff in whonix workstation such as torrc and var/run/tor/control are just there for tor browser and have no effect to gateway tor.
I haven’t ever seen advice that it’s recommended to restart Tor before use of certain apps. Don’t recommend to invent that unless there is a strong rationale for it. Might not have the effect that is expected.
After successful NEWNYM, there is no need to change any port. After NEWNYM, Tor won’t be re-using the same circuit. That’s the point of it. Just make sure the application was properly shut down as NEWNYM cannot influence long running established connections. Thereby as I said, the following would provide higher assurance:
Giving anything in the WS the power to restart Tor would be dangerous because it can help a network adversary figure out who the target is if they have malicious code that modifies Tor connetivity in visible ways.