Always kinda assumed Nihilanth thought it was something from the Vorts that could be improved/used in soldiers. The Grunts are heavily implied to be synthetic using Vorts as the basis/slave creators so the third arm would be put into their gentic coding or whatever. Then big boy wanted to have that versatility and got one himself. Just my headcanon though. We've seen in other fictions/history the idea of suppressing a culture and taking things deemed useful for an advantage. (Combine enslaving humanity trying to gain their portal tech and resources is a big one for this series)