The blessing names three things at once, spirit and soul and body, and asks that the whole of them be kept together. This reaches toward the deep human longing to stop being split into warring pieces and to become one.
The writer, Paul, does not pray for the spirit alone, as if the body were something to escape. He asks for the entire person to be made whole, nothing left out, nothing pushed into the dark. That is the real work of a lifetime, gathering every part of ourselves, the honored and the rejected alike, and letting them be reconciled into a single, undivided self.