I have the exact same problem, but I assumed I was too stupid to work out how to configure Github to stop this and didn't want to waste any more time trying to work it out so I just turned the emails off.
I work for a fairly large org with lots of Github repos which I occasionally contribute to and there seems to be no way to configure emails alerts in a manageable way – I must either get an email for everything or ignore everything. And ignoring everything is obviously preferable when the signal to noise is this bad.
Sounds like the same problem! I'm working at a large org, was involved in setting up lots of repos, therefore I end up getting pinged on so many of them that I'm no longer directly working on or directly interested in.
There's also not a bulk method anywhere (that I can find) in Github that can deal with unsubscribing or changing settings on many repos at the same time.
I work for a fairly large org with lots of Github repos which I occasionally contribute to and there seems to be no way to configure emails alerts in a manageable way – I must either get an email for everything or ignore everything. And ignoring everything is obviously preferable when the signal to noise is this bad.