It absolutely affects spine.It isn't due to the stiffness of the material used for weigh(static spine.It is because more of the weight is going behind the balance point and weight toward the rear stiffens the dynamic spine.Your balance point is always ahead of center so full length,internal weights put a disproportionate amount of weight behind the balance point.
Adding full length weights also change the position of the balance point.If you have a well tuned arrow,changing the balance point,changes the tune.
Now if you add the full length,internal shaft weight before tuning,that's a different story but it is hard to predict how much point weight it will take to tune the now stiffened(dynamic spine)shaft.