Having /etc/ssh/sshd_config not do what it appears to do is inexcusable, however that comes about.

Even if the fix is no more than structuring the file a little differently so there are parts both before and after the .d loading, and comments that say what overrides what, and all the actual config files and default behavior are still the same.

You shouldn't need to edit an undocumented file that's force enabling an insecure authentication method in the first place.

"You're using it wrong" doesn't change the fact that the defaults are poor and likely to ultimately cause more devices to be improperly configured than if it was left as sysadmins and end-users expect.