If Article II says that one must be a natural-born citizen to be eligible for the presidency, and if a natural-born citizen means a citizen at birth, then logically one must look to federal law at the time the person is born in order to determine whether such person is eligible, but Congress isn’t “amending” the Constitution when it modifies the rules for citizenship at birth any more than it amends the Constitution when it admits a new state to the Union. Please note that by looking at the law in effect when the putative president is born it prevents Congress from passing retroactive laws so as to make Obama eligible or to make McCain ineligible.
In Goldwater's case, the argument was that since Arizona subsequently became part of the territory of the 48 (?) states, he had a defensible position. I could never tell whether that drift came because it was increasingly viewed that he did not have a chance or whether the lawyers who said that thought it was the correct answer.
McCain has a problem. And I don't expect it to get to the election or even the conventions. And in a mutual challenge, if the facts prove Obama is out on this issue, the temptation on the trier of fact will be to kick McCain out too to demonstrate that it is not a racially motivated or partisan decision.
Your second point is something that has been inferred but I don't think anybody has said straight up--but it is unquestionably correct in my view. Natural born, even though he wasn't when he was born but Congress in legislation changed the form of his birth? I doubt it. They could amend the Constitution and I suspect they probably will but I doubt they go all the way to the end of permitting a person born out of the country who gets to be a citizen only through a naturalization proceeding to become President but that is just speculation.
McCain would be an easy fix by the amendment process though.
Or we could just annex Panama...