For Microsoft, they are all under the same Microsoft account. So I guess these big boys have special contracts.
The truth is that we actually do pay, as we have private repositories. We ask that people prepare their initial open source releases during a 30-day window - making sure they have a decent README file, the right LICENSE, Code of Conduct, etc.
Full disclosure, I work at Microsoft within our Open Source Programs Office and I own our billing relationship with GitHub for the large organizations including Microsoft, Azure, etc. We pay via a yearly invoice for a set level of services today but we're always looking for better ways to collaborate with GitHub!