You're coming at this from the perspective of "it's weird to change the rules after the fact" which is reasonable but not how stare decisis works. The principle is that once something is decided once, it should be decided the same for all other parties litigating the issue unless and until the precedent is overturned. If something hasn't yet been litigated, it is still an open question.
It would be weird if, for example, the Supreme Court said that gay marriage is constitutionally protected but all the existing laws banning it could stand because they were enacted earlier.
It would be equally weird if the Supreme Court said that gay marriage is constitutionally protected, but states that have previously successfully litigated challenges against their laws can keep forbidding it..
On the contrary, I'd expect the Supreme Court to say exactly something like that when it suits them. The Supreme Court throughout history has invented as many hoops as they needed and then jumped through them in order to appeal to political winds and public opinion.
It would be weird if, for example, the Supreme Court said that gay marriage is constitutionally protected but all the existing laws banning it could stand because they were enacted earlier.