Do I understand correctly that GitHub currently doesn't support SHA-256 repos at all, so the author faked a screenshot of what the create repository UI would look like if they choose a really stupid way to add support for SHA-256 repos, and then proclaimed it an unsolveable problem? Selecting the repository format based on the first thing pushed to it is really not a crazy idea.
The submodule problem is real, but the forge problem is entirely just "if forges implement support in a way that makes it painful it will be painful", and that's true of literally every feature that requires forge support.
github does support sha-256 repos in some kind of private beta. https://github.com/bk2204/talk-rust-in-git is one of them.
but yes: that ui in the article is likely entirely imaginary, but it's likely an option (either in the ui for private beta users or by raising a support ticket or by some internal tool) to get sha256 repos today.
I also don’t know how big this problem really is. You practically have two ways of creating a repo. Local first and push or create a repo remote with Readme etc and clone.
The submodule issue is a different beast. But that one is currently a problem as well when a person choose a http url or ssh url. I have some extra git configs to normalize everything to ssh for instance.