Yes, that is correct and exactly what is happening, which understandably so, can be inconvenient in regards to the new Unity’s Prefab System and for which I do look at possible solutions.
Populating blackboards via code can certainly work. As long as the blackboard variables populated are of the same type and have the same name that the graph nodes or tasks parameters are looking for, it should work without any problem.
Once again though, I do look at possible solutions around that using the new Unity prefab API, or even by changing the serialization of blackboard variables.
