I wonder if your MIA target is Jake Finch? Under normal/vanilla circumstances, he either gets dead or returns to Finch Farm prior to you getting control of the settlement. So whether he's natively counted in the population there or not is hidden behind the Ironworks quest. I wonder if Conqueror's alternate method of settlement takeover is butting heads with the Out of the Fire quest.
That is very plausible. In the past there has been an issue with kidnapped settlers being made into defenders since the radiant quest triggers before you talk to the settler or go there, making it impossible to complete since they'll be in some far off dungeon. I don't know if it has been solved, though it has not happened to me in quite a while. I haven't raided Finch Farm in quite a while.
If KAH doesn't solve it then it's very likely that Jake Finch is a defender. I would try using console commands to bring him over. I'd use:
- Prid 00045c37;MoveTo Player 0 0 3000
This moves him to the current cell since I believe they have to be killed in the same area and 3D data loaded for it to count, but far above the player so they will die from fall damage. I don't use cheats unless something has gone wrong making it impossible to complete normally.
When I returned to the settlement the first time Jake Finch had recovered, I killed him and the rest of the finch family.
I suspect that leaving the settlement after the raid has begun may cause issues. If the defenders are not Persistent, any data that may be being tracked by the scripts may be lost if they are unloaded(ie if after beginning the raid you go far away or enter an interior cell). The best I can suggest is to try loading a save during the raid or just before it and moving Jake Finch to you via console commands, since I suspect that going to Saugus Ironworks may break the scripts.
It takes a few minutes to fully explore a level 3 settlement so scripts should have run their course during that time, also, I have a very high-end PC which should be able to run scripts quickly.
In typical cases you would be exactly right but the game engine is very, very old and Sim Settlements basically takes stuff 1000x further on the engine than ever intended or ever imagined. The game engine can unfortunately bottleneck even such builds like 2080 Ti & Threadripper with game installed on NVMe(Over 3000mb/s read), making it generally not possible to have perfect performance on 4K. It will work but FPS drops will still happen and such mods like Scrap Everything will still tank performance. The game engine needs significant changes to work optimally with the latest hardware, currently it can't fully take advantage of it.
With scripts and loading data, most of it is tied to FPS and since FPS is usually capped at 60 it cannot go faster than a certain point. Physics and load times are also directly tied to FPS. On Skyrim Special Edition people have found a way to allow FPS above 60 via Havok Fix, it's something that could be interesting if it's possible on Fallout 4. Another scenario I have not heard about yet is using a RAM Disk since that can offer read/write speeds even higher than an NVMe SSD, it's unfortunately very hard to fit the entire game on a RAM Disk since my install for instance is 120GB. I've tried with RAM Cache but my current system does not have enough RAM to take advantage of it.