Crystal Tower is kind of different in that the plot of 5.0 and especially 5.3 makes no sense if you don't do the CT series. We've seen before with Coil that some dialogue changes if you've done the content or not, which seems simple to integrate Gabranth into the MSQ if he's not fought in Bozja and is instead relegated to an "As you know, Noah van Gabranth was the Legatus of the IV Legion, he broke from the Empire and blah blah blah", and removing the "As you know" if you didn't do the content.

Otherwise, I see no problem with his storyline continuing in the next expansion as a sidequest, especially if it involves Dalmasca or Lea Monde.