Probably going to need to wait for better mod tools and documentation to be able to play any further on my 200+ hour save. I have zero desire to go back and replay two of the more tedious mission chains from scratch, to the point that I've already spent more time trying to fix the broken save than it would take me to play back to where I am now. Learning the console--from scratch, since I didn't play much of any Skyrim--is considerably less tedious than reliving a bunch of dialog I've already seen or having to deal with more lockpicking than necessary*, no matter how good one gets at it.
I'm at the limit of what can currently be done via console commands I think. I cannot force start the two mission chains the bug I ran into is preventing me from seeing as they depend on timers that have already expired or dialogs that can no longer be triggered.
The way Starfield handles this stuff is a major step backwards from many previous Bethesda games. For example, in Morrowind and Oblivion, being where one needed to be and doing what needed to be done resulted in requirements being satisfied and quests advancing, even if one go to that point in a manner that could not easily have been predicted. In Starfield, there are hard triggers that aren't supposed to be able to be bypassed...you cannot just go where you know something is, or stumble upon it accidentally, you need to get there in a specific way the game has planned for. Even breaking through doors, teleporting around, adding quest items, or resurrecting/resetting NPCs via console can't trigger the events I'm missing.
Since I was trying to avoid spoilers, it was at least nine hours of play time until it became clear something was wrong, and could easily have been much, much, longer. For example, if I had kept my save where I originally attacked The Hunter immediately after meeting him, I would have put another 150 hours into the game before I realized The Hunter was a critical NPC with critical dialogs that could not occur if the Hunter was hostile before the very end of the game.
I'm pretty annoyed at not being able to see the rest of the story in a way that is reflective of the choices I've made in my play through. I've been railroaded into a dead end by a lack of play testing done on interactions that should have been obvious; I'm where I am now because I had my character attack other characters that clearly presented themselves as hostile.
*On the topic of lockpicking; there is no such thing as an enjoyable lockpicking minigame. This is doubly true for Bethsoft games, where the minigames are ridiculous and often unbypassable (if you want to open the container/door). They bear no resemblance to any concevable actual lock (which are not designed as puzzles for theives, but as security measures to deter them) and have become increasingly used as a way to gate content behind stupid skill tree unlocks. My character has been able to pick master locks since before they left Kreet, and I've picked many hundreds of them in this game. I can do most Advanced/Master locks with no assists in seconds at this point...and I get more and more annoyed at their existence with every additional lock I encounter. It's probably the most absurd and grindy aspect to the entire game.
The last Bethesda game to not totaly botch locks was Daggerfall. No minigame at all, just a skill check against lockpicking, and there was almost always the option to just smash the container or door open, at the cost of noise, which is the most plausible way to handle things.