MSQ

[linayar]

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.

Maybe there was a change in plan, but even if true, I think that might have to do with the popularity of the character.

Regardless, once they decided on what to do with the character, they need to preserve the continuity of the story, which means the tower is relevant for 5.3.