It's not a very elegant solution but you can simulate screen touches using adb. There is an answer that covers it here - simulating touch using ADB
Edit: Adding some details on using adb to dump a file of all of the UI elements.
In the android sdk in the platforms/android-L folder there is a tool called uiautomater.jar that adb can use to run tests (though I've never used it for that) and to dump an xml file of the visible elements.
adb shell uiautomator dump test.xml
will create the xml file (on the device not your computer) that you could then look through in your code to check for the pop up you want. If you want to interact with the pop up then you can use the coordinates given in the xml dump to pick which one you want and use an adb touch event to click it.
Not a pretty solution but hopefully not too difficult to work into your tests :)
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