The system cant give powers, it only unlocks previous powers of the shadow monarch, its a system built so Sjw can slowly get used to the power instead of dumping it all in him all at once
in the novel the architect himself says while fighting that it was a duplicate body but after the shadow monarch didin't sutface with the black heart he probably became able to attack the soul or something like that and the reason he couldn't control the system was the system was made based on the powers of the shadow monarch so he blocked him out[/spiler]