This is an old problem that's affected my Structures mod for years. Now that its city generator is nearing completion and I'm in the process of designing a new city with large buildings, this bug is the last thing standing in the way and posing a huge blocker to my project.
Minetest doesn't seem to properly handle spawning large schematics as part of newly generated chunks. I tried using both minetest.place_schematic and minetest.place_schematic_on_vmanip from the minetest.register_on_generated function but both come with a huge problem: The schematics are always incomplete with large cubic chunks ripped out of them. This results in every city being completely mangled to the point of structures making no sense. The bug doesn't seem to affect smaller structures at all (roughly 20 x 20 x 20 and under) even when they're being spawned rapidly, it's primarily just big schematics.
Here are a few screenshots showing this issue with the new apartment blocks I'm working on. You can see the interiors of apartments as they're randomly sliced open. Instead of the weirdly cut out cubes, we should only be seeing solid walls with windows from the outside.



