I just don't think there's any meaningful claim that CI explicitly configured by maintainers using officially supported channels should be lumped in the same category as automated scraping of repositories for creating PRs.
Sure, there are many definitions of automation that would include both of these things, but I think it's obvious what GitHub intends in practice.
Perhaps they didn't mean automation per se, but CI is certainly automation, automatic merging, as in not manually merged by a human.
Perhaps a better rule would have been, no automation on repos not controlled by yourself.
Ps. Another reason why we mostly host on BitBucket ;)
Checking that pull-request and comparing the URL of the user with the blue avatar, you notice that the username marked as "bot" is actually an App [1] but the user [2] — linked at the bottom of the right sidebar — is a regular GitHub account (with no "bot" marking). I am not sure how are they different at a technical level, maybe the App is a web-hook and the User is the one interacting with the API. In any case, they are two different things.
I created a bot that would scan for private SSH keys to connect to AWS and other services, it also warned about leaked software licenses for SublimeText and other popular programs at the time. While many people appreciated the initiative, it was not taken the best way by others. Ultimately, GitHub suspended my account and I had to explain what was all about.
One year later, through my employer, I created another bot to scan for security vulnerabilities in projects written in Ruby, Python, PHP and Node.js; this time I already knew that I would need to contact GitHub beforehand to make sure what were the limits of the "automation". They simply stated that — at the time — no automation was allowed, which was quite surprising because CI is automation. Travis and other services are allowed to do things there so I didn't understand why my bot was different.
I reported to my employer that we would need to shutdown that project and move on to something different. One year later, I find that GitHub implemented a (semi) vulnerability scanner for a selected group of programming languages, warning the repository owners about problems with their software dependencies. I cannot be mad about this, it's their service, but it still made me a bit angry.