So if I understand, you are facing the error that says: "Cannot create an instance of the object type 'sprite': there are no instances of this object in the project.", but you're not willing to place an original instance anywhere in your level ?
What I have done on my side is creating a "garbage" level, that has no use in the game itself, wherein I place one instance of every single object type.
You only need to create one object in the whole project, not one per layout.