That's not really what's going on. Those "native" APIs you mention in most cases just call back to Java APIs under the hood. For better or worse, most of what Android is is written in Java. There's no hidden "C++" layer of Android to access.
In theory it is possible to write raw Binder calls to various Android services, skipping JNI in many places. However, it is basically rewriting the entire OS API and structure from scratch.
You can generate binder wrappers from aidl, that would work. This is fairly common when doing platform work (for those like me who work on the operating system rather than on apps).
However, this would be a terrible idea because usually the android api is stable at the Java wrappers (I.e. ActivityManager), not at the aidl level, which would make this very fragile for app development across a multitude of devices and platform versions.
