Wait a second. This probably isn't going to be fully answerable until we have Claude's rapports if at all but him being explicitly unaligned brings up FASCINATING questions because either
You can be summoned/created by a goddess and then choose not to work for them or make a pact. Would fit Claude and Corrin's roles in their original games hence them being the two that are unaligned but still disciples
While Dimitri and Edelgard are summoned this is just a Furry AU version of Claude like Ephraim/Ike/Robin(?). Interesting because that would essentially invert the dynamic of three houses where Claude is an outsider coming into a conflict, here Dimitri and Edelgard's conflict is coming to him. Except you know they're not trying to kill each other
NEITHER goddess is summoning/creating ANY of the returning characters, someone else is (the player? The original goddess? Are they not summoned at all the goddesses are just memory wiping people who exist in-universe) and the goddesses are just lying to get them to help with minimal resistance and Claude, Corrin, and maybe Robin now that I've checked the flavor text and see if doesn't specify for her, weren't caught by either when they woke up so they wandered around and had enough context that by the time one of the sibs showed up they were like "ehhh no thanks." That would actually fit with how Robin meets Chrom in Awakening.
I'm interested to see if there's a specific reason they directly state Claude is unaligned rather than just not mentioning it like they do with the others. Also again idk if they chose a different word in other languages but "disciple" does directly mean "follower or adherent" which raises the question of how one can BE a disciple if they're explicitly not following either goddess. Which if an intentional language choice might point to option three where all the disciples are actually disciples of the original Goddess whose treasure Naga and Fenris are looking for.
I am gnawing at the bars of the lore cage
I finally got my mitts on Claude's BB (see here) (thank you gintax from fescord)
Hmmm… I don't really understand any of this. It seems I have no memories at all.
Well, I have no choice but to live with it this way. There's work I need to focus on here.
I'm a warrior of the Divine Dragon Naga. I'm here to help defeat the Demon Wolf leading people astray.
This could be a challenging mission. It's a good thing I've got a knack for developing strategies.
Anyway, that's how things look from where I'm standing. You can count on me to handle it.
At least, in his light side BB, he's said explicitly to be with Naga. Either way, he does have the disciple-typical amnesia. So perhaps "unaligned" doesn't necessarily refer to "not aligned with Naga or Fenris" but "not aligned with any particular group"? Like how Lyn is associated with Sai and Shea. Did Naga just set him loose...
Either that, or the light side BBs are not canon, either. So far I think we've all been viewing it as one of the BBs is canon, and the other one is a what if (like Hati's light side BB would be a what if, same as most characters' shadow side one). But perhaps netiher is.
Then again. For the so far third faction characters (Uka & Tamamo), both of the BBs have been similar enough in content that you can't write one off as a what if.
Congrats to Claude for being the only 3H lord on Naga's side lol.
As for the point abt the creator god: there is zero lore and i doubt there ever will be, but I still personally believe the only creation of the creator god, their proxy, is the player character. Every playable character is your disciple, fighting for the cause You The Player have decided to support in the bid between Naga and Fenris, which is why the BBs are often phrased to be Talking To You. Unlike Kieran, though, this new god is a complete non-entity in the main story, so.
In that sense, since the creator god is dying/dead, and their successor is You, i would highly doubt any of the disciples were brought in by them, unless it's a Heidr situation. (Heidr for fesh....? I do love Gully. Gully in fesh would be kinda awesome. Make it Seidr/Gullveig actually.)
Other note is that for both Lyn and Dima, there was Some Sort Of Summoning Ceremony, so they're definitely not just random people from this world.