Turns out there's at least one other CK draft of the Orion screenplay, according to Orion and the Dark producer Peter McCown.

Charlie Kaufman wrote the script and I’m such a huge fan of his. How did working with that as the base come about, and how was it working on something that fans might not expect from him?

Peter McCown: Yeah, I mean, Sean and I are huge fans of Charlie’s work. We talked about it all the time. I studied Charlie’s scripts when I went to film school, so he got this wonderful book from Emma Yarlett, this Orion and the Dark high concept, and I think he really sank his teeth into it. This was years ago. He produced a couple of drafts of the script, which he just expanded that world.

I think he’s so strong in the kids’ space, and I really hope he continues a little bit more in the kids’ space because of his whimsy and his creativity and the expansion he can do to really anything with introducing these new ideas, but then tying them up so brilliantly. I think he’s perfect for this, and he brings a little bit of an edge to it that you want. It’s not your stock animated fare anymore. I think he brings it to a different level, but also, most importantly, with the main character, he’s able to explore main characters in this and in his other works that are extremely real and extremely complex. I think you don’t always get that in animation. My hope and my dream is that he continues in the kids’ space for sure — at least in the family space. (Source)

That's via ComingSoon.net. "Working with that as the base" seems telling. I'd be interested to see how different the second draft was to the first, considering how far the movie wanders from the first draft. Here's the accompanying video:

Then there's this, via MovieWeb:

MovieWeb: Orion and the Dark is an amazing film. I really enjoyed it. Charlie Kaufman's script teaches children how to face existential crises. Talk about getting him to adapt Emma Yarlett's book. What was he like to work with?

Sean Charmatz: He wrote the script. And we kind of took it from there. We loved the script. We were excited about the themes and what the movie was going to be about. I was all for it. I'm so happy that we got to make this film because it's a film that is brave. It is unique, tonally, it is a little edgy and scary, and deals with things that are not always topics people want to talk about. But I think we did it in a really whimsical way. I think that the film could help people to actually deal with their anxieties. (Source)

There's a video with that one, too.

To me (though I could be wrong!) "we kind of took it from there" implies that, yes, CK's script was essentially a starting point only. Also interesting that Charlie isn't doing any media for this one, when he's done it for every other project--he never even mentioned Orion when promoting Antkind and Ending Things, though The Memory Police, IQ83 and others were happily chatted about.

Not suggesting anything sinister! Only that Charlie isn't as attached to this film as it's been sometimes implied.