Yes, you can build as "Android" app and cordova APIs will work as long as "cordova.js" script tag is included. It was mainly meant for building apps with intel.xdk APIs, Cordova 2.9 support was later added, Cordova plugins are not supported in this build.
"Cordova for Android" is in beta release, this is more like an actual Cordova app built using Cordova CLI, Cordova plugins will soon be supported, intel.xdk APIs are not supported. You have to include "cordova.js" script tag for Cordova APIs to work. This will become the default build for Android in future.