Another difference is that this won't be the first time that they will be coming into possession of extra limbs and senses. Because of this, controlling the extra pupils and arms is easy for them to do. It is practically second nature for them.
Of course, the extra two eyes and two arms are not enough for Legion. Currently, they have too few body parts to go around. It is definitely going to cause some arguments among them.
The matter of who gets to control what is a serious matter, but one thing they can all agree on is that they can't go out and be seen like this. Once they are seen like this, it will prove that they have two pathways.
So they shut off one pathway and only left one active. The one they decided to shut off was the pathway of undying. This caused the golden pupils and the extra arm to disappear.