I think I already know the answer but it is possible to use the Android app from the Play Store on the RC Pro or do you need to go the Amazon route only?

You can install the app via an app installer like apk pure.

I think they only support the amazon version from what Ive seen.  

Yes you can do both but if you want a beta version then You can use amazon store

Does anyonw know this problem; when you start a mission (Waypoint flight) in Litchi on the smartcontoller, Litchi get closed by start the flight.