Holy shit is…..

I doubt it was a homage, since “crystals are magically powerful” is a common trope and “black means evil” is similarly common. Just parallel development.
 
But yeah I was certainly recalling Crystal Tokyo with those scenes.

In Sailor Moon R, Crystal Tokyo was struck by a black crystal that killed almost everyone. The palace was the only safe haven from the corrupting power of the black crystal. King Endymion provided assistance to the past sailors while Neo-Queen Serenity was frozen in crystal, using the silver crystal to protect the palace from the black crystal.
 
The villain that sent the black crystal down was Death Phantom, a criminal that was banished away into Planet Nemesis by Neo-Queen Serenity and became one with the will of Planet Nemesis.
 
Aside from his grudge against Neo-Queen Serenity, Death Phantom’s goal in the arc was to destroy the Silver Crystal.
 
There are entirely too many parallels not to think this two-parter isn’t a homage.

Well, the whole series started of like a magical girl flick…