This, and also Android's overall userspace design is kind of idiosyncratic. I'm sure there are other legitimate designs of a Linux-based mobile OS, which don't rely so heavily on Java and a virtual machine. Ubuntu will be Qt-based, for example. That throws out the possibility to reuse the Android application framework.
Ok, but there's nothing that prevents them from implementing QT on Android using the NDK. You don't have to throw out all application compatibility to achieve something like this.
If I remember correctly then it can also run Android apps in the same WM together with other apps. It actually shouldn't be too hard to replace Android's WindowManager with some other implementation (say, QT-based) due to the nature of Binder (Android's IPC mechanism).
Haven't they merged the "android kernel" into the linux kernel recently?