I think doing the opposite is better usually, never making changes to the main /etc/ssh/sshd_config and always add your own customizations to /etc/ssh/sshd_config.d/; that way you have clear separation of your own and distro configs, which makes life easier especially when upgrading sshd. Although I'll readily admit that I don't myself follow that advise all the time.
This. And give your drop-in a prefix like 00-*.conf.
Fwiw I don't think SSH adds the include line upstream. Most distros add it now.
Yes. I had a hard time figuring out if a low numbered prefix got final say, or the high numbered one.