This'd be an issue if the 13th became a bigger setting in the story, but I don't think it will, now or in the distant future. We will most likely be done with rescuing (or failing to rescue) Azdaja and dealing with Golbez in the next two patches, and then Zero, if she is still alive and kicking, will most likely stay behind to try and make the 13th her home again. Then can more content be added to the void questline as side content that will take into consideration what the MSQ has accomplished.