I started another play thru from scratch. At the overseer's desk in vault 111, after you open the evacuation tunnel, it's the city manage holotape 2078 that gives the notification that it is applying performance changes. (Do i have any holotapes? Don't know. I ain't got pipboy yet.)
I continue on with the game until I get near the exit. I waited at the pip boy, but didn't pick it up, for around twenty minutes or so.
I decided maybe I missed the completed notification (the notifications go by so fast) or maybe it just won't finish until you get above ground. IDK. I put on the pipboy. (I have no holotapes in my inventory.) And I went ahead and exited the vault.
Then, I went straight to Sanctuary, talked to Codsworth, killed the insects, and opened the workshop. The notification that the City Manager Holotape had completed it's business popped while I was talking to Codsworth. (I made a save to mark the the game time: 12 minutes after leaving the vault save, and 45 minutes after the exit cryo chamber save.)
Only then did I make the trek to Sunshine. When I got there, it was fully functioning, full of civilians, and preexisting debris was scrapped as expected. (Wasteland Survival was missing, I assume it has been moved to the workbench.)
The only thing I've done different this play thru is removed Egret and Far Harbor Settlements from the settlement build list, waited longer than usual to leave the vault, slowed my roll, and opened Sanctuary workshop as soon as possible, instead of just skipping it.
In my previous Conqueror starts, I've rushed through and out of the vault straight to Abernathy, Starlight, or Sunshine eager and curious to see what's going on at the prebuilt settlements. In all of these previous play thrus, I've managed to get to one or more of the prebuilt settlements before the performance changes that started in the Vault have completed. And, although city plan structures are more or less built, every settlement has been a ghost town and none of the original junk seems to have been scrapped.