In an interview with Skwigly, an online animation magazine, Orion and the Dark director Sean Charmatz says Charlie wrote three drafts of the film, and they used the third.

How did Kaufman’s script find its way to DreamWorks?

I think DreamWorks is aware of the whimsy and the inventiveness and the charm and depth of Charlie’s writing and they were like, “let’s try and make an animated movie with all that stuff in there,” and I commend them for that. He wrote three drafts and we loved the third draft which came to me a few years after he had written it. I put together this animatic, where I was the voice of Dark and my son was Orion and I made this four minute piece based on Charlie’s script. I showed the studio and they loved it. (Source)

Charmatz also talks about a few of the changes that were made.

There were things we had to cut out. There was a whole page where Charlie listed the titles of films with Dark in it, because Dark was talking about how he’s hated. Charlie took the entire script page to name films. Obviously, in the movie, we can’t spend 10 minutes listing titles of movies. No one’s going to sit through that but it’s still really fun to read it.

That could’ve been pretty fun.

It would have been 10 minutes of listing, just a static shot. As an artist, I love that, I love how pushed that is. It’s really inspiring to me. I love that statement.

And of course, being an animation magazine, he talks about the visual aspects of the film as well.

I'll be posting Charlie's first draft in a day or two, but if anyone has a copy of later drafts by him, I'd love to take a look. I wish I could see what the third draft looked like, before the 24 other credited writers and story artists did whatever they did. Maybe they suggested ideas and wrote material that didn't make it into the film, and the businessy contractual side of things meant that they got a credit anyway? And it turns out the film really is 90% Charlie? WHO KNOWS.

Thanks to the ever dependable u/pavingmomentum for the article!