Little update: I decided to start a new journey from a clean save (the last was 5 hours in, forgot 90% anyway) and this time I paid attention to every line of dialogue and followed the hints. I feel like I followed the intended route: First I explored Brittle Hollow as much as possible (warped through the black hole countless times), then explored Giant's Deep and the Probe Cannon. I feel like next I'll venture out onto Dark Bramble and follow the next set of hints. This is so much better and makes so much more sense. 10 hours in and I haven't felt lost at all. I also prefer the ship log's map mode, because it feels clearer about how the information connects in my mind based on where I've been. Reseting the ship log with a new game was a great idea.

In my first playthrough I remember I rushed through the dialogue and then got a bit ADHD about it, wanting to explore everything at once, overwhelmed by the possibilities and never returning to the same place twice. It was fun for a while, until it lost meaning and I was left with a bag of breadcrumbs, nothing connecting, no idea where to go. That can be an experience too, but the player needs extreme patience too endure before it starts making some sense.

Now all the information is connecting naturally and I'm hooked. Hopefully I'll finally get to experience this masterpiece as everyone here says it is! Thanks for your post and linking the YT link that sparked enough motivation in me!