Finally got caught up with this thread, and now I have things to say. Generally, I think all the features in this blog post are great, but I have a few suggestions that I think would make them better. In order of how important I think they are:
Reloading after battle as a story point sink
I know that sounds crazy, but I think story points can be used to create an ideal middle-ground between iron mode and save-scum mode. Story points are the perfect price to pay in order to reload and revise history. They could be used to undo crippling defeats, but they're difficult enough to earn to disincentivize tedious reloading. As a fourth-wall-breaking method of influencing the game, it makes perfect sense that story points could be used to revise history.
This could be implemented in such a way that a story point is lost even if the game is shut down 'unexpectedly' by saving SP somewhere other than the save file, preemptively deducting one point whenever a battle starts (GUI would not show the deduction), and refunding the deduction once the game is saved. This way, one SP would be lost any time a player fights a battle they choose not to save on the first try. I'm not sure what the best way to handle cases where someone reloads without having any story points in the bank, but there are workable solutions, such as SP debt or removing progress toward the next SP.
Problems with permanent hullmods for SP
I love the idea, but in practice, I don't think it will work out much better than simply spending SP to increase a ship's OP. People are likely to choose the same hullmods whether they're permanent or not, with the caveat that low OP mods will be seen as inferior picks. In the end, the only difference between a ship with permanent hullmods and a ship with additional OP is that one is more flexible. But how meaningful is that flexibility? Why would someone want to remove the mods they think are most important for that ship?
The OP discrepancy problem could be solved by making perma mods grant 1x/2x/3x/5x bonus OP while still deducting their normal OP cost, but we'd still be left with the bigger problem of perma mods failing to make ships unique. No matter how I slice it, I can't think of a way that perma mods could be made interesting and different without modifying their efficacy. Elite hullmods with improved or supplementary effects could work, but people would still choose the same hullmods. A Dominator would just graduate from Heavy Armor to Elite Heavy Armor, which I don't think is that interesting. A more interesting approach, I think, is to make perma mods less effective versions of their temporary counterparts.
Retrofit hullmods - Permanent hullmods with normalized effects
The problems with permanent hullmods could be fixed by reducing and normalizing their effects in such a way that they're roughly balanced in spite of all having the same price (0 ordnance points and 1 story point). This would make choices about hullmods much more interesting, because the best mod for the ship is no longer the best choice for a perma mod. You don't want a Dominator to have retrofit heavy armor, because then it couldn't install the normal heavy armor hullmod, which grants a better bonus.
Interface for finding markets that are selling a specific ship
I imagine this could work well as a bar event as long as the selection of find-able ships is limited. Players could find some sort of broker or informant at bars who would offer to give the location of a ship chosen from a list of x randomly selected rare ships. I think this could be a very good QoL feature. Scouring the sector in a frigate in search of ships I want has never part of the game I enjoy.
On the name of Story Points
The name is serviceable, and I cant think of any great alternatives, but I worry that new players will suspect that story points are a substitute for actual narrative, given how open-ended Starsector is.
Some potential alternatives: Influence, Narration, Fortune, Kismet.
If it were up to me, I'd call them "Machina Points", as in "deus ex machina" (a contrived solution to an obstacle in a narrative). Partly because that's exactly what they are, but more importantly because the meaning of "machina" is ambiguous and somewhat obscure. Normally I'm all for clarity, but story points have such a nebulous purpose that it's impossible to give them a name that clearly conveys what they are. I think this is one of those cases where you have to choose between giving a false impression or no impression at all. Other loosely defined words could work just as well.