Hello James,
It is possible to use Google Compute Engine only without using any Google App Engine. In fact Google App Engine flexible environment runs services on Compute Engine VMs. You can see the comparison between App Engine flexible environment to Compute Engine here. In addition to that if you are using App Engine flexible environment (i.e. “managed VMs”) it always required to run one instance constantly despite no request are coming in where as in standard environment it can come down to zero. You can calculate billing for using the Google flex environment instance for your configuration by going to the Google Cloud Platform Pricing Calculator. If you notice the billing estimate for the App Engine flexible environment instances matching with the billing you are getting it means Google App Engine flexible environment instances is not serving any purpose of your app. If you are certain that Google App Engine flexible environment is not serving any needs to your app or you do not like to use it for your app, you can go to the link here to find how you can stop the instance or you can go to the link here, where you will find instructions how to disable an app in Google App Engine.