Previously the Smartphone edition was only publishing to the iOS configuration file and the Android app was using this. When we provide the updated Universal Android build, it will use the Android specific config file instead of using the iOS one.
Yes, you will need to tick the Android option for the Smartphone edition. After ticking when you create your next issue, you shouldn't need to tick this again. We auto tick the options for you based on the most recent issue we can find (ordered by deadline date)