mayb having to write a tool script in godot to replace specially named empties form blender with instances of gameplay related scenes or sth.

Why did I never think of that. My level designer is gonna be so excited if I ever remember to write something like that myself.

I think this even has some direct support from Godot to automate it. The EditorScenePostImport class is supposed to be used for stuff like this i believe but im not entirely sure (i haven't tried or had to try anything like this yet never mind automate it, i just found this while looking through the documentation on 3D scene importing).