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For the most part they are currently linking to the nightly w3c editors drafts. Is that the right thing to do? Looking at the shadow dom spec, it seems to link to a mix of W3C TR latest published versions as well as whatwg html spec.
The right thing to do depends on which political model you subscribe to. Best for implementors I'd say a mixture of WHATWG and W3C editor's drafts. E.g. for DOM I'd refer to http://dom.spec.whatwg.org/ as it's actively maintained whereas its copies are not.
I'm assuming that the MSFT folks prefer not to link to whatwg. I'm just going to fix the permanent redirects from dev to w3c nightlies for now.