I don't know if you will run into issues running both on the same system. But, if you want to control HG from a different application, you can use a couple different approaches (web API, MQTT).
1) web API: you can send the command to HG to control modules or return status however you need. You will need to interpret the response in your other application, but it's generally a simple text format so that should not be a problem.
2) MQTT: HG has built-in MQTT to talk between HG machines, but I see no reason you couldn't use this with a different system to communicate using the same protocol. Alternately, you could create a new MQTT app that would interpret bi-directional communications as needed.