I am using Cordova 5.1.1 and email@example.com for geolocation, which uses - cordova-plugin-compat for its Android 6+ permission needs.
When the permission popup is open, Cordova reasonably fires a "pause" document event, as expected, signalling the view having left from the app to the popup (cordova.js):
// Volume events
cordova.fireDocumentEvent(action); // action being "pause"
The solution, upon inspection, is not to do anything in the $resume callback that obtains geolocation permissions.