I don't like this, because then it means I have to change my repo to make a Github feature work, when Github has whole configuration UIs on their site for both my account and my repos.

Also I don't see the problem with opt-in. If your bot/plugin/service is worth its salt you'll be putting some effort into marketing it (which includes explaining how to use it).

The alternative is Github marketing the opt-out, which seems a bit strange if they're launching a feature and advising users how to not use it so they don't get spammed.