The majority of APIs are not exposed to NDK users, only to OEMs.
Google could release lets say Android 8 with another POSIX compliant kernel and the only apps that would notice are the ones using non official APIs.
Currently, Android is released using Linux kernel, ELF executable format, POSIX API's, and so on. There is no Android/kFreeBSD, nor Android/NT.
Android games can be launched on Linux using android libraries (not all, but some works pretty well, see: http://www.shashlik.io/showcases/ ).
Linux tools can be launched on Android systems (including X based tools, if X server is running).
For most of practical purposes, Android is Linux.
Debian user space isn't the same thing as a kernel.
Android kernel doesn't expose the same syscalls as a standard Linux.
I am really keen in having Google replacing Linux with Magenta, then we can carry on this discussion about what Android is supposed to be.
Compiling and using a vanilla kernel instead of the distro one is straightforward and easy job for people with basic knowledge of source building. It's not a job for "very few brave souls". The reason many people use distro kernels is because they're good enough.
OTOH any consumer Android device requires millions of loc patching to a several years old version of Linux kernel just to boot.
And, frankly, if Google decided to swap out Linux for, say, DragonflyBSD, almost no-one would notice or care.
Where in Android, you just get Java and a tiny bit of C and C++.
Check the NDK documentation, Google provides a list of the set of APIs any NDK application is allowed to use.
Since many used to ignore that list, starting with Android 7, any app that uses unauthorised native libraries will get killed.
