What Prefixgate shows is that a W3C standard is not a rigid set of laws like the 10 commandments. Rather a W3C standard is like a peace treaty - all adherents agree to respect certain protocols and behave in certain ways, buy are free to pass whatever laws they want within their own boundaries. Assuming that these proprietary laws do not conflict with existing treaty stipulations.
Peace treaties give us access to the best of both worlds: vendors are free to innovate as they see fit, yet they still commit themselves to some level of interoperability. Innovations influence the standard and the standard ensures that all vendors adopt the best innovations at some point.
The comparisons between IE of old and Webkit are incorrect. Microsoft has a history of implementing standards incorrectly (http://www.quirksmode.org/css/quirksmode.html) and bullying standards bodies (http://techrights.org/2011/09/06/michel-levy-comes-out-swing...). When it comes to standards Microsoft does not act in good faith.