What happened
This is regression - it used to work in 5.2.x, but doesn't work in 5.3 and 5.4
When we adding SpawnablePrefab to the list on the NetworkManager - it doesn't mark scene as dirty and you can't save these changes

How we can reproduce it using the example you attached
- please see attached video
1 Open attached project
2 Open scene sc1 and select GameObject in the Hierarchy
3 Go to inspector and in List Of Spawnable Prefabs add Cube
4 Open scene sc2
Actual result: no popup window saying "You have unsaved changes" and List Of Spawnable Prefabs is not saved
Expected result: when you adding Spawnable Prefab - the scene should be marked as dirty and you could save it