Hmm,the whole scripts are there but the modules in a core only affect the core.Although there would be some bleed over for more general modules but things like transcendental connection in medici would only work for the goals/objectives of medici but if you take the module it would affect the whole sub and other subs you stack it with.Same for rebirth which is in every core but would only affect things related to the core it is in while if you put in the module it would affect the custom as a whole and other subs you stack it with.
Last paragraph said only the structural scripting is removed
Reason for adding modules even if its in the core