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It doesn't make a whole lot of sense to me either. The only thing that really reconciles it is if there were other plans for the meta-world that got scrapped somewhere in the writing of Alliance or the transition into Chiru. The conflict that Meta-Ange believes exists does not exist at all anywhere else in the stories. While it kind of makes sense that Bern would pull an Ange of the future into the story, if we take Meta-Ange as somehow representative of an "actual" or "Prime" Ange, it doesn't make any sense that she'd believe that she can actually do anything to "save" her brother as such.
I mean, she already clearly realizes in the St. Lucia backstory that her family can't come back. Even if the Meta-Ange bits are read as some kind of faint hope of someone returning, they couldn't possibly return through any acts that Ange herself can actually take. And the whole idea of "well they might return to an Ange that isn't you" only makes sense in the context of Prime-Ange realizing that the family could be "saved" in a story but that this would not actually save anyone in her world. Which is obvious. I mean, Ange's not that dumb.
Regarding the other point, Amakusa was kind of like... what was his deal, anyway? Seriously he has essentially no purpose whatsoever in Chiru. He's basically a confused question dispenser for parts of Dawn and barely matters at all in Twilight.
For something that was such a huge chunk of Alliance, I just can't help but think the Ange stuff wasn't going to become what it eventually became and initially meant to set up something else that didn't get followed through on. Same thing with the Maria stuff. The Beatrice-Maria-Rosa dynamic is set up pretty strongly as a major thematic issue, but then Maria scarcely matters in any way until Requiem. And the themes about the Black Witch don't really follow through there either.
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