I have a lot of suggestions.. But here's the one on my mind right now.. Allow Blueprints to be apart of Scenarios. Maybe in the Blueprint list they'd show up as part of the Stock BP's.. (Or Scenario BP's if there is the desire to add some UI to it, but I'm trying to suggest the easiest way.) It shouldn't be difficult to implement.. When downloading the Scenario from the server, add <ScenarioName>/PrefabsStock to the list of folders downloaded... and Saves/Cache/<Game>/SharedData/Content/PrefabsStock to the list of blueprint folders to scan in.. This would have a lot of benefits to potential scenario writing... Putting themes on ship types, and I can think of ways that JUST adding this feature would make it possible (in a way) to purchase ships from traders...
That only shows up in creative though, so people would have to re-save it from creative to use it in survival.
If it is for specific blueprints that can be used by the player, then it is different. It is an interesting idea but I think it should be followed with a switch (yes/no) in difficulty settings to give the freedom to everyone to use whatever they like without hassle, as it is now.
I'm not sure why a toggle would be needed for it. Servers can already disable factory spawning if they want.