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Let's separate the OpenCV problem and your configuration problem.
There's a very simple short code in OpenCV which checks if compiler accepts NEON. https://github.com/opencv/opencv/blob/master/cmake/checks/cpu_neon.cpp what happens if you just try to compile this code ? no CMake, just type
aarch64-linux-gnu-g++ cpu_neon.cpp
what happens ?
you are specifying CMAKE_TOOLCHAIN_FILE using $CMAKE_TOOLCHAIN_FILE variable. What is the contents of this variable ? Where is it setted ? is it pointing a correct file which actualy exists ?
In the issue comment, you show a command using "sudo cmake" why sudo ? sudo is only required for installing, never for cmake
Thanks for the detail docker, but where did you install the cross compiler ?
Why are you making a symbolic link of opencv ?
ln -s /opencv/opencv-3.4.0 /opencv/opencv
what if you don't do this symbolic link part and directly work in the directory created by unzipping ?
BTW, why aren't you getting tar.gz instead of zip ?
And, why are you trying to build using docker ? It's way easier to build directly on real ARM 64bit devices. It's just a 40$ or so and you'll have much much less problems.