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The part I've been waiting for years to hear was:

"We recommend sending IE9 the same standards-based markup your site sends other browsers. "

Does it mean I don't have to use separate code for IE and Standards based browsers?

Yes.

For how long? Can I count on IE9 keeping up with the new developments in HTML capacity, as we move closer to desktop functionality?

Of course not - so IE9 doesn't matter, since it will soon be obsolete.