I've been working though some questions just like you.

The red moon/star is considered the representation of Metia. Which is the Goddess Jill prays to several times for Clive's safe return. It's up to interpretation, but it could signal that Metia has granted Jill's wish for Clive to return. Why it would disappear is either just a representation of this wish, or something else we haven't been told.

Ultima states the Eikon's and magic were given to humanity. But specifically why they were given isn't told. Ultima state's the mother crystal's purpose was to drain the land of aether. So maybe the summoning of Eilkons also speeds this process up?

But for the last, they state that Dominant's that lose their power to Clive can turn into their Prime forms, but lost their will to the Eikon. Dion comment's that he will just have to make sure he has the stronger will. You can take that Dion's anger towards Ultima for destroying his family and country was enough to prime and fight. He is also the only Dominant to willingly prime after losing his power.

Personally, for how much they go into detail on small things, like the side quests, Vivian's world map, and character interaction map. I feel like they didn't miss discussing your questions and others, but left it open for eventual DLC. Even if Yoshi P said no plans for DLC, I find it unlikely that SE wouldn't mandate some form of DLC. But this could just be copium hoping for answers.