I think they should just add a line in the UI instead of hiding the info deep in tickets or issue, but that's a mere communication issue. Overall, it's not surprising, and actually good for the user.

On letsencrypt.org:

     In Progress:
     These large providers are currently rolling out support for Let’s Encrypt for custom domains.
     You may or may not be able to enable support in their control panel,
     or you might notice certificates have recently been issued for your domains hosted with these services.

     Blogger
     GitHub Pages

https://github.com/isaacs/github/issues/156#issuecomment-366... https://community.letsencrypt.org/t/web-hosting-who-support-...

and so on.

> I don't think it's a major problem, but it does violate the Principle of least astonishment,

The principle of least astonishment should tell you that in 2018 HTTPS is becoming the default and hosting web pages with automated HTTPS should be expected.

What you should be astonished about is that it took Github so long to support HTTPS everywhere.