Right off the bat, as far as I'm concerned, Superman should always be the only Kryptonian survivor.
Realistically, now, in the boundaries of a movie, they don't have to be specific at all. The story is about a dying planet and its last son. They'll go that way and find some hole to pull Supergirl in, should they decide to go with a Supergirl movie (and, hell, assuming it'll be a Kara Zor-El one).
As for Zod? The Phantom Zone is a whole different beast.
Well you should qualify that then.... If you say last Kryptonian survivor than that means Zod et al are gone. It means the bottled city of Kandor does not exist. It means Kara dies on Krypton. It means a whole bunch of potential stories you can tell are gone. If you say last son of Krypton then it works better because he was just born at the time of destruction. In the comics for over 50 years, he has not been the last Kryptonian survivor. He was just the last son of Krypton.
If they have to go back and find a hole to allow Kara to exist then it means the original story had a plot hole and it means the original story was weak. Id rather they just acknowledge the possibility that there were other survivors even if they don't say it outright. I think that is a better way to proceed..... A safer way to proceed.