MSQ

[Arkevorkhat]

The tower is integral to the continuity of the story in 5.3, so that's a direct relation. There is a limit to how much expositional dialogs can help explain when it involves the fate of a character.

The tower is only as integral as the devs decided to make it.
Prior to 5.3, it was basically optional, but conveniently, when they added level 50 content to the free trial, they also made it mandatory to do crystal tower for the story.

Absent the financial pressure from Square-Enix Corporate, I can all but guarantee you that the story of 5.3's post-MSQ would have been very different.

I don't know if you remember, but prior to 5.3, the whole "send this guy back to the source" (Speaking vaguely because spoilers) idea was shot down multiple times, and then suddenly with 5.3 they decided "No actually, we ARE sending him back."
If anything, adding the Crystal Tower to the story requirements introduced plotholes, instead of patching them.