I am wondering if it is possible to launch applications (behaviours)
developed in Choregraphe from within application developed using
Pepper Sdk for Android Studio?
No, there is no API for that, and as far as I know there is no plan to add one - the two aren't intended to be mixed.
And what will happen to the behaviours installed on Pepper when I try to run app installed from Android Studio?
There shouldn't be any conflicts between the two; if you're using Autonomous Life's focus, focus can be on either type of application, they can coexist on the same robot. It's just that the two technologies are not intended to coexist in the same application.