In the event that the Mysterious Figure is actually G'raha Tia and he's suddenly relevant to the MSQ i really doubt that SE is gonna be like "ok so you have to do this raid that used to be optional but now you have to because otherwise you wouldn't understand the plot".
My bet is that it would be something like this: the events of the Crystal Tower happened. Even if it wasn't your WoL's story it was a story that happened. The game already states that there are many high level adventurers around that could fill parts of our role and i don't think there's anything in the CT storyline that demands the presence of the actual WoL. So if you did it prior to the story moment where it becomes relevant then the game acknowledges that you where there and you did it and seeing G'raha is a reunion moment. But if you didn't then they would need to stop for at least a moment and explain the important parts to you. But the thing is if the CT plot actually becomes relevant they'll probably stop and summarize it anyway because for a lot of people that was ages ago.
It can be a bit... clunky but there's a lot of simple ways to integrate it into the MSQ without demanding a detour from a chunk of the players.