I don't understand how the combat AI is supposed to work.
Welcome to the club.
More generally, it feels like AIs don't factor in helping other ships in difficult spots.
As far as I'm aware, each ship AI explicitly only considers themselves and have no sense of what other friendly ships are doing from a strategic or tactical level. They don't even really have a sense of how to move around each other (you will often see a frontline ship at full flux trying to back off, while a backline ship behind it trying to move forward, and so the two of them will just kind of stay there, unable to move around each other). So yes, even if you the player knows that the ship can safely move forward because there's another ship that's in front of it under attack, the ship will happily stay back at zero flux until it feels like "the time is right" to move in. That's true even under aggressive personality.
Moreover, there seems to be some sort of "tipping point" where a ship decides it's time to go all-in and commit to the fight. So you'll often have some ships running in and trying to fight, despite being at high flux, while other ships nearby will stay back at zero flux and unsure of what to do.
I tend to use large, long range ships because it's easier to set them in a line (i.e. with fewer ships, it's less likely for them to block each other) and since they're killing ships at longer ranges, they're less likely to get fluxed up and lead to these AI issues. This leads to more consistent outcomes. The other option is to lean in on mass zerglings, i.e. LP Brawler spam, since the LP Brawler is so fast that it can quickly move away and it's so small and maneuverable that they don't really block each other much. But other than the LP Brawler, few SO ships are good enough to do that since SO severely cripples their offensive potential against difficult enemies.
In this case either an eliminate, escort, or rally/defend command behind the enemy would get them moving in the right direction.
Yeah unfortunately even "eliminate" does not mean that the ship will move forward. Attached is a screenshot of a Sunder (Sunder 10) where, after being given an eliminate command, and starting off near Sunder 7,
it decides to back off to over 3000 su away from the closest threat (notice that it's over 2000 su away from me, and the closest enemy ship is the Radiant which is around 1000 su away). It may be due to flux levels but ships, under eliminate order or not, will happily move in at over 80% flux, so this is inconsistent behavior. Nor are there missiles or fighters nearby that would cause it to back off. This is under 0.97a-RC6.
As far as I'm aware, this is not new behavior introduced by the update, the AI has had this behavior in past versions as well (staying back at zero flux while other ships are under attack in front, unable to move around each other, sometimes backing off when given eliminate command, etc.). There's no feedback from the AI as to why it engages in this behavior, so the root cause is always difficult to figure out.
What's known is that the AI is usually overly afraid of and overly prioritizes missiles and fighters, so on ships that lack PD, it'll tend to stay away (and that may be a reason for the "tipping point" -- farther ships decide there's too much stuff to go in, while closer ships see a juicy enemy target and decide to go in despite all the stuff). But putting PD on your ship leads to another problem, namely that the AI under aggressive personality sets its positioning range based on the weapon with the shortest range, and PD weapons often have short ranges. So if you put PD on a ship, it'll decide to close in to melee range, even if its main weapons are all long-range weapons, and even if the PD is there just to make it not be scared of missiles/fighters. There's not a good way around this AI issue; but the reason why I put LR PD Lasers on my Conquests (in addition to forcing autofire on) is that it's a PD that has a relatively long range, to discourage closing in too much.