Precisely no one, including the Chinese, believes this. So what was achieved by maintaining this fiction?
This is not meant as a naive question. I recognize there are plenty of occasions in diplomacy, as in life, when it is inadvisable to tell the unvarnished truth. There are even occasions when it is mutually beneficial to maintain a patently false facade so that both sides in a diplomatic crisis can save face (see "This is Why Governments Don't Comment on Intelligence Matters"). But how does this situation qualify?
One possible justification is that such a blunt denial shuts down any potentially awkward questions from the media. But he's the U.S. president. He can handle it, can't he? And surely the whole point of lifting the embargo is to send a signal to China, so why would he want to avoid questions anyway?
Perhaps the clinching reason is that Obama simply didn't want to speak so openly while in Vietnam and while standing right beside his Vietnamese counterpart, who has a delicate balance to maintain in relations with Beijing. If that's the case, perhaps Obama will speak more openly after his departure.