There is no "special" access in GitHub, and no person as far as I know has such an access. I work at Microsoft, but GitHub side is very detached so I don't think there was any collaboration.
It would appear there's a backdoor system for them.
The OP used a workaround of starting a new GitHub project a couple of project renames, and a project transfer - which did generate a flurry of notification emails.
(I’m surprised the “move into enterprise account t” action doesn’t at least notify all owners on the account. If it normally does, and these ones didn’t, that’s a super bad look for both the foundation and GitHub…)
The workaround "project transfer" used/suggested for getting back _out_ of that enterprise account gets explained in the article like this:
1) Create a new GitHub organization, normally. For example, name it new-yourorgname
2) Rename your organization in GitHub Enterprise in the Settings to something like, dnf-yourorgname
3) Rename the organization from step 1 to your desired organization name. You want to complete this quickly after step 2 so no one takes your organization's name.
4) In the GitHub Enterprise dnf-yourorgname go into each repository's Settings and transfer the repo to the brand new yourorgname organization.
Not at all surprising that generates a flurry of emails, especially since in the authors case step 4 needed too be done 44 times, once for each repo in the org.