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Sorry I missed this - this is expected and should be fixed with #1933. https://aa-turner.github.io/peps/ has the theming branch applied, and both issues are resolved.
From https://python.github.io/peps/, all of the links to PEPs assume the domain as the anchor, not the subdirectory. For instance, the index links to PEP 621 via https://python.github.io/pep-0621/ when it should in fact be https://python.github.io/peps/pep-0621/.
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