Yes! I mention this in my hour-long Ascian video, I just didn't go further into it because A: I haven't read the book, and B: it's not clear if or how that's relevant. But on the actual morality of Amaurot... yeah, it is worth noting that even the book it takes its name from says that there's no way it can be perfect, I believe even the book ends with outright saying 'that sounds nice but it's only a story and cannot exist'.
While I agree, we are in a weird spot there where nothing we know of could cause those things, so by nature if we fight the Soundmaker in Endwalker it does kinda have to come out of nowhere. That said, there are a few angles:
A: Just... wait, play a longer game. Introduce elements that pay off later.
B: Make for more of a thematic thing; FFIX has Necron come out of nowhere because he's an embodiment of death, and the whole story's about death*. Make the Soundmaker an embodiment of a significant theme of the story (say, the cycle of persecution to extremism to persecution, or the sins of previous civilizations), it won't feel as out of nowhere.
C: Get referential. Even if the Soundmaker comes out of nowhere, people won't really mind if it's Lavos or something; they know Lavos, so they can shortcut the whole explanation themselves.
D: Introduce a disciple or aspect of it, then lead back to the Soundmaker. This one I'm guessing they're up to; Fandaniel knows things we don't about the End of Days, so he's in prime position to lay down the path leading to the Soundmaker so it's not from nowhere.
*As an unrelated thing, I do think it would've worked better if FFIX instead went for their original idea and made Hades the final boss. I think they went with Necron instead because he's more neutral and the story isn't about dealing with the notion of 'you might go to hell when you die' but rather 'someday you will die' in general, but at least the benefit of Hades is everyone can recognize he's a Death Thing, while with Necron it can be lost on someone.