They can handle G'raha in exactly the same way they handled Estinien (depending on whether you'd done DRG quests), Allisae (depending on whether you'd completed Coil): a minor, one-off piece of dialogue. It could be something like:
- Have not done CT: My name is G'raha Tia, and I have been keeping watch over the technology kept within the Crystal Tower, waiting for the day it would be needed. Now, I have emerged because etc etc etc
- Have done CT: It's good to see you again, my friend! You may be wondering why I have left my post at the Crystal Tower. As it happens, I have emerged because etc etc etc

Others have mentioned time travel, and that would make things even cleaner, as far as G'raha is concerned. Whether you know him already or not, he could know YOU, since it's a future version of him. It simply presumes you'll do CT sometime in the future, if you haven't already (even if the player never actually does so during their tenure playing this game). It would be spoilers for his eventual fate in that plotline, but whatevs.

IN GENERAL, however, the devs have long, LONG since decided their stance on this: They just don't care, and will not spend much effort on keeping players from getting confused about what happens when. Players themselves are responsible for figuring that out, if they do events out of the order they were introduced. There will be no hints given, and no assistance of any kind for the potential confusion this can cause.

The first instance of this occurred when you had the ability to serve a delicious meal to the Sultana during the CUL job quests, even if she's supposed to be deceased (e.g., do the CUL quests after the dramatic cutscenes ending ARR, but before the Sultana is found to still be alive in HW). There have been other instances since, such as Estinien, Allisae, and Nero.