That's by-design, and it's why no one should ever use Microsoft GitHub -- because you don't own your data, Microsoft does.

Very good reason not to use those, if they are critical to your business.

This speaks to one of my secret desires, I've worked at a bunch of small companies now where the workflows were all ad-hoc and I feel like even at bigger companies there are persistent failures to "understand Git"... one of the most pernicious being that, most companies have a modernist "this is prod, it is one place running one codebase" approach, Git is postmodernist "here is this project, there are many branches showing different perspectives on what this code could be", most CI/CD systems in my opinion sit at the interface between these and choose the wrong side to be on, they choose the Git side -- "we ask every branch, 'do you want to deploy yourself to prod?' and if it says yes by virtue of having a CI.yaml file with a branch filter naming itself to be run, then we deploy it to prod."

So what I want is kind of to build a company that's just strongly opinionated about that... "everything is in one Git repository, the `main` branch is authoritative for ACLs and CI/CD config, the bugtracker writes issues directly into that repository and has an ACL role that allows it to do that, the RFC widget writes your code design docs directly in there as well, we do rebase but we merge without fast-forwarding, you have to use semver and it works like this..." and probably nobody will use our offering because "GitHub is more trustworthy" but "if anybody does they'll love us" haha

Fossil does this within the repo, maybe we need a way for Git to do so too.

You can host your own on your own site. Most major open source projects have their own website anyhow. They really don't need to be on github or gitlab to begin with, just roll it yourself like the rest of your website. The only reason why people do it is because its a meme at this point to have a github (and even gitlab, if only as a foil to github).

Like the internet itself?

git on ipfs and issues stored in a literally plaintext file

Why do you need a centralized hub? Most repos on github are entirely unrelated to eachother. Repos can be self hosted. Issues can be tracked on your own website. You don't need a megacorp to run a website. If you are writing open source tooling you are more than qualified to roll your own here.