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How about codebase that were uploaded to GitHub, by someone other than the original copyright owner?

e.g. I can clone the GNU codebase and publish it to GitHub. Clearly I don't own the code and do not have any rights to grant GitHub a license.

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Section D.3: "If you're posting anything you did not create yourself or do not own the rights to, you agree that you are responsible for any Content you post". A lawsuit against Github has no standing for the scenario you suggest, because Github is not at fault.

Does that mean if anyone posted my open source project to GitHub, I can fill a DCMA takedown request regardless of the license I chose?

Well, I don't think it's a DCMA issue, but it does very much depend on the licence you have chosen. That's what the licence is for, to allow people to use the code that you have copyright of, and to define what they are / are not allowed to do with it.

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