What data is being transmitted? Is the data encrypted at rest and in transit? Is this called out anywhere in the Scirra terms of service?
Good question, I think we do not know much about this but you said
"How is the security of our information/code being handled during minifying?"
I assume it's the same security we get when we generate the AAB/APK when opting for their service.
But if the code is really sensitive, then there's always a way we can download the Android Studio file, the Cordova file, or the XCode project and export the output ourselves.