The proposed solution is bad, the file will be restored by the package manager at some point. Always prefix your override files with '99-' or 'zz-', this would have prevented the problem.
For OpenSSH configuration the first directive controls, not the last. So if you want to set an option make sure your include filename comes lexically earlier, not later. This is why the Include directive is at the top of distro-installed /etc/ssh/sshd_config. You can verify your server configuration using `sshd -T`, and a client configuration using `ssh -G`; they dump the resolved configuration to stdout.