I actually reached out to GitHub support about this because I’m in the same situation: I have unsubscribed manually from all my emails, and the unsubscribe link returns 404.
Got this as a reply (which is how I figured out it was because of NixOS):
Thanks for reaching out to GitHub Support. I’m sorry to hear about those unwanted emails. I believe that these are “onboarding” emails sent to admins in new accounts, which in you case appears to be the NixOS organization. We have heard from other members of the NixOS organization and well and are looking into this. As for unsubscribing, were you trying to do this from a mobile device? We have heard from other users that the mobile unsubscribe link returns a 404, but the same link on desktop will work. If you are unable to unsubscribe still let me know and I can forward the request to unsubscribe all of your email addresses.
I’ve asked them to unsubscribe me manually, let’s see if that works on my case.