You're pretty much correct. Larian appears to have put player freedom over establishing basic narrative structure, and it means that everything feels oddly disconnected. It doesn't help that Larian didn't really commit to doing stories with impact and then letting players miss out on them. I'd say Larian had a lot of ideas they wrote down early in the process -- a plot with so many quests you can skip, a party member has the McGuffin -- and then remained too committed to them even when they began to really work against their storytelling. The video about the difficulties Larian had with the Astral Prism is the most obvious point of evidence. As a professional writer and editor, if you're running into a problem like that, where you basically have to do a ton of work to make something work in Chapter 6 (the Prism ending up with the player) and about the worst thing you can do is insist on keeping the plot as-is. In that case, you should go back to Chapter 1 or 2 or whatever and just... make it work there, when the audience is primed to expect contrivances to set up the drama. Just have the artifact end up next to you on the beach, y'know?
Then you've got at least one variable pinned down (where is the artifact and who has it) and then you can start planning some structure to your story.
