That's just not how it works, and it never has. One of the main purposes of the .d files is to avoid modifying the distro's sshd_config file, so you don't have to resolve conflicts during an OS upgrade. Commenting your overrides in the sshd_config? That's backwards.

Downstream distros sometimes want to override the default settings. That's what .d is for. It doesn't violate the dogma "principle of least surprise", especially if you run `man sshd_config` and learn the first thing about sshd's config files.