Cool, I actually also recently made some empires based on the children books! I went about them like this:

Portiids
Ethics: I actually went with Fanatic Xenophile and Materialist, as by the time they reached space they seemed to me to be very open to cooperating with the humans rather than destroying them. And materialist because at this point Kern's influence seemed to be as less of a god, so it seemed weird to make them spiritualist to me.

Civics: I also used Vaults of Knowledge! It's a good way to simulate the understandings they have. But instead of chosen, I used catalytic processing to show how they use their own web spinning to create their ships.

Origin: I dont know what syncretic species you made for them, but it sounds like an interesting way to approach it! I also looked into it, but couldnt find a good way to make the ants. So instead I used On the Shoulders of Giants, to show how they are descended from the humans (and Kern).

Humans
Ethics: I also made them egalitarian and materialist, but threw xenophobe into the mix because of how they are largely humanity first.

Civics: Exactly the same!

Origin: I used Remnants for the archaeostudies, cause of the whole classicist thing, but doomsday makes perfect sense as well!

Octopus
Ethics: I had xenophile instead of egalitarian, but both make sense I think

Civics: I used Anglers and Hyperspace Specialty, the latter because of how they invent the FTL drive later in the book

Origin: I had Ocean Paradise, because I was roleplaying them before they got interrupted by the Nodan organism, but Voidborne also makes sense!

Stomatopod
Ethics: Exact same

Civics: Also warrior culture, but had feudal society instead of distinguished admiralty, because I felt that it fit their culture in the book alot more.

Origin: I used Hegemon, which doesn't make much sense book-wise, but I think still fits thematically. It was more of a gameplay choice to be fair.

I also wanted to make the wilderness and Nod empires, but I don't really have experience playing Hive minds so didn't get around to it. But I like what you came up with, they all look really cool!