One workaround you could do is to set accessibilityLabel to a conditional value depending if you are building for debug or production (or just have some global flag to indicate that). While not ideal, it will minimize code changes and will allow you to access elements for testing.
However, I would like to ask you a related question... I was not able to set accessibilityLabel which could map to content description for Inputs and Buttons (TouchableHighlight / TouchableOpacity elements). I could see content-desc field in UI Automator for other elements but not for anything actionable. Have you been able to see / access those elements in your test??