On the idea that the blocking may have been automatically triggered, I believe this is unlikely since GitHub was blocked using separate methods, introduced at different point in time. Generally, automatic blocking doesn’t affect a whole website but certain URLs containing sensitive keywords.

The real challenge for the GFW authorities is HTTPS. GitHub is unblocked for now, but their temporary blocking of it didn’t change anything. Because it’s encrypted, they can’t selectively block content. You can use GitHub to publish any content and the only thing they can do to stop you is to block the whole site. Which, as you point out, has commercial consequences and so they’re reluctant to do it. Very interesting to follow.