Article II, sec. 1, cl. 5 does not say that the president must have been born in the U.S., it says that he must be a “natural-born citizen.” You are correct that Congress cannot modify that constitutional qualification, and that that Obama bill saying that the children of military personnel should be deemed “natural-born citizens” is legally meaningless, but the fact remains that constitutional scholars for many decades have interpreted the clause to mean that the president must be a citizen at birth (thus, “natural-born”) as opposed to becoming a citizen later on (”naturalized”). What matters is what U.S. law says when the person is born.
BTW, Barry Goldwater was not born in a state, he was born in Arizona in 1909 when it was still a territory, and no state kept him off the presidential ballot in 1964; George Romney (Mitt’s dad) was the child of U.S. citizens born in a Mormon commune in Chihuahua, Mexico, and his foreign birth was not an impediment to his 1968 presidential run (he was on the ballot in the GOP primaries); and Albert Arnold Gore was not born in a state, either (he was born in the District of Columbia), but no one questioned his eligibility during his 8 years as VP nor when he ran for president in 1988 and 2000.
Regarding John McCain, he was born in the Canal Zone, which was a U.S. territory, and federal law stated that a person born in the Canal Zone that had at least one U.S. citizen parent would be a U.S. citizen at birth; unlike babies born outside the U.S. with one citizen parent, the citizen parent of a child born in the Canal Zone did not have to have lived a certain number of years in the U.S. in order for his child to be a U.S. citizen at birth. Of course, both of John McCain’s parents were U.S. citizens and had lived all of their lives in the U.S. (except for time abroad while in military service, which, according to federal law, is counted as time residing in the U.S.), so John McCain would have been a U.S. citizen at birth even had he been born in the middle of China.
One point that should be clarified regarding U.S. military bases and embassies located in foreign countries. While they are usually described as “sovereign ground” of the U.S., they are not U.S. territory for purposes of U.S. citizenship laws, and a child born in a U.S. military base or embassy abroad is subject to the same rules for determining U.S. citizen at birth as a child born outside of the military base or embassy. Children born in Guantanamo Bay Naval Base, for instance, are not U.S. citizens unless their parents meet the citizenship and residency requirements applicable to children born in any other foreign land.
The real bottom line is that in my view, the Supreme Court is likely to come down on the proposition that "natural born" as used by the framers in the Constitution means born in the geographical United States. I think that continues to be the general view of most of the Constitutional lawyers who have looked at the question.