I agree the hole at the top does not appear to be related to the root, especially since no roots appear to protrude into/from it.

I would probably just chalk it up to the calamity, particularly the severe shifting of aether in the land that lead to the dramatic change in Eorzea's landscapes. Either a tree that size existed and then most of it was destroyed (between the shifting of the aether and the 5 years of time between the calamity and when ARR begins, it would be believable that the land where that tree was could recover), or the calamity caused a tree similar to the surrounding trees near that root to rapidly grow, and then the majority of it was destroyed, etc.

I don't recall any trees of that particular size in the black shroud prior to the calamity, so I'm leaning towards the latter over the former.