I think the best solution for updating Kali chroot would be a configuration management tool e.g. Ansible (ansible-pull), Salt, Puppet.

In this way it is possible to change the chroot, while keeping nearly all user changes untouched.

If you then provide a separate Kernel update flashable via recovery. And the nethunter app takes care about everything in android. And has a option to trigger the configuration management tool.

OK just my thoughts about this