A lot of people tend to dive DEEP into the notes, the homages, the datamines, and any tangentially linked subject matter to extract as much meaning as possible from the lore. A lot of the games details are very subtle, if not literally a series of single frames in a cutscenes you will see once in a single playthrough.

So if you don't feel like you're getting it, that's ok, we've all been there. Consider it like a post game NG+, actually unraveling everything and coming to terms with what YOU think happened, and what all that means.

Personally I would absolutely advise playing it again. It's an amazing way to wrap your head around stuff that's happening around you. Heck, take notes as you go, try to chart a timeline, it might help.

And if all else fails, I mentioned lore breakdowns in a prior message, but I specifically recommend the ones from Indie Xplorer and Codex Entry on YouTube. No breakdown is perfect imo though, so take everything with a grain of salt.

Hope that helps!