I am not an expert in the store (now I just develop the apps!), but, what App Builder provides are various BAT files (talking about Windows, also creates SHELL files for Mac OS, to be used in the same way and for the same purpose). These files names are "debug", "run" and "release".
When we execute the "run" BAT file Apache Cordova generates a debug APK of our apps, and, if we have a device connected to our PC (or an iPhone connected to our Mac OS), after the APK for Android (or IPA for iOS) is generated the app is launching in the device.
To do the above we just must connect our device in the computer, if everything is ok (the drivers are ready, etc.) we can use the "run" BAT to compile and launch the app into the device, so this is the best way to debug the app in a real device.
If we have no devices connected and execute the "run" BAT file, Cordova try to launch the device emulator configured in the Android SDK / Android Studio. I told you this is the best way to debug the app... but talking about the device... because normally we can debug the app in a browser, which is more easy and fast. Only when need to try something that only works in a device... we need to test it in the device, of course.
Then we have the "debug" BAT file (or SHELL file). Executing this Cordova prepares a "debug" compilation of our app that we can copy to our device or another, etc. It's the same than "run", except that with the "debug" the app is not launched in any device nor emulator.
Finally we have the "release" BAT file (or their SHELL version for Mac OS), and, when we execute it what Cordova prepares is a release compilation of the app. This generated APK is ready to be uploaded in the Android Store.
In order to get a release, if I am not wrong, we need to sign the APK, so you need to fill the App Options -> Cordova -> Android -> Signing. Once you fill the edit boxes that you can see there, App Builder generates the right JSON file, which Cordova uses to sign our apps.
Probably I miss something that you can be interested in, so, please, go ahead if you have any further question, and, I will try to help you as best as possible.