Android Apps are and mostly always have been restricted to the Java virtual machine (or its modern equivalent) exactly because that makes them portable between sometimes quite different base systems from different vendors. If you insist that makes it less of a Linux system I'd like to know what you think of flatpak apps on top of immutable distros. I hope you agree that, conceptually, they're quite close actually.
Nothing of that is expected to be supported on NDK, at least officially, Google and partners have the freedom to break those expectations as much as they feel like it.
Many computer users run a modified version of the GNU system every day, without realizing it. Through a peculiar turn of events, the version of GNU which is widely used today is often called Linux, and many of its users are not aware that it is basically the GNU system, developed by the GNU Project.
There really is a Linux, and these people are using it, but it is just a part of the system they use. Linux is the kernel: the program in the system that allocates the machine's resources to the other programs that you run. The kernel is an essential part of an operating system, but useless by itself; it can only function in the context of a complete operating system. Linux is normally used in combination with the GNU operating system: the whole system is basically GNU with Linux added, or GNU/Linux. All the so-called Linux distributions are really distributions of GNU/Linux!