Loose threads

[NegativeS]

I can't answer all of these, but...

1. The Dark Crystal

Almost certainly just a representation of Zodiark. Can't imagine they had the Endwalker model ready to go that far in the past.

2. Hydaelyn telling Minfilia to stay behind

It was stated that Minfilia was one of Hydaelyn's most devout followers, and was thought to have been chosen for that reason.

I don't think Hydaelyn intended to kill Minfilia when she turned her into the Word, nor do I think it was wholly Hydaelyn's will when she sacrificed herself to save the First. Either way, if she didn't sacrifice herself, the First almost certainly would have been rejoined, which may or may not have weakened Hydaelyn to the point where she would either die, or be vulnerable to the machinations of the Ascians.

3. Zenos' source of power

I believe the power he had came from the swords he had at the time. At the very least, Ame-no-Habakiri was said to have been "crafted ... by Susano himself and was bathed in the blood of an arcane fiend." Definitely powerful.