For 'Super 23 Royale' I didn't want loads of large scene files in the buld - initially the target platform was also going to include mobile. To overcome this I wrote a tool that would be able to save what objects had been placed in the scene, there transform values and then load that data at runtime.
The scene is populated with empty parents, for different categories of objects (eg: ground, buildings, terrain). Prefabs are placed as children of these transforms and positioned/ rotated. Each object must be a prefab to be able to save a link to the game object for spawning.
Using the scene in the videos below as an example, the file sizes are:
Saved scene with prefabs - 3.95MB
Saved scene without prefabs - 93KB
Scriptable Object with prefab data - 359KB
Doubling the amount of prefabs in the scene approximately doubles the file sizes, to 8MB for a scene with prefabs, or 718KB for just the data.
The scene can then be safely reloaded in the editor to be worked on further. The same data is passed to the scene loader at runtime, which loads everything ready for the player.