To reproduce:

1. Open tests project from attached project or from: Unity/Tests/PerformanceTests/NestedPrefabs
2. Tests which show bad results: SceneOpenTests.OpenSceneWithBigNestedPrefabsWithOverrides
3. Run it from Unity Test Runner as any test.

Results:
Prefab has 1 child, 5 components each game object.

with 100 instances in a scene, it takes about 80 ms to open the scene.
with 100 instances in a scene while each instance has property override, it takes about 3500 ms to open the scene.

for comparison, with 4000 instances in a scene and NO overrides, it takes 1000 ms to open the scene

Could be improved