Yes, I've structured the project so that both the Android and Open Pandora are built from a single tree. Next on my agenda is getting that tree to closely mirror Richard's repository in structure. Currently, Sven (ecsv) is doing a great job keeping the two repositories in sync, but with my limited git/ mercurial knowledge I would have trouble maintaining it if he were to leave.
My ultimate goal is that the "AE" project will be only a front-end project (for Android, Open Pandora, OUYA, GameStick, etc), with a thin JNI interface for the Android versions. Through a series of pull requests, build-flag activated pipelines should be built into the upstream repositories for ARM, GLES2, and Android/ Pandora-specific things (like the way it is done for Windows, Linux, MacOS). It will take some effort to get to that point, though. In the mean time, Open Pandora will still be much more "in the loop" than it has been.