It's pretty much identical at a high level: there is a proxy layer that is much like a message passing system. A component (web view, JS engine, etc.) says, "Take a photo with the camera" and the proxy layer calls the native code needed to take the photo with the camera.

The actual camera data is just abstract data, it doesn't care if it was generated from a JS call or from a native call.

PhoneGap and Cordova are, at the core, just a standard proxy layer and plugin API. The other "pure JS" solutions have their own custom layers.