We don’t need namespaces. We already have scopes.
Within the scope of the content I’m authoring, [me too](#me-too) can unambiguously link to # Me Too. I as an author should not have to think about any containing scopes. This is perfectly analogous to block scopes in most programming languages.
It is the responsibility of the embedding context to respect and protect my scope. Whether in its rendering it avoids ID collisions by altering its IDs or mine, or demotes my heading levels to avoid multiple H1s, it is its business, its job to make it work.
There should be a clear separation of concerns between authoring content and publishing mechanics. I shouldn’t have to manage the technicalities of an output format while authoring in a format that is supposed to be independent and portable. As the content author, the only thing that matters is that I have a semantically unambiguous and intuitive way to create internal links. I don’t care how they are ultimately rendered.
The one case where I do care, when I want the world to be able to deep link into my published content, I make sure to choose a publishing tool that produces predictable, “exportable” header ids and deep links, perhaps one that retains the unaltered CommonMark anchors or perhaps one that doesn’t. Who knows, maybe the content will get published in a relational database, and all anchors get translated into foreign keys. These are publishing concerns, not authoring concerns, not CommonMark spec concerns.