I missed the mark of Shawn’s question apparently. I was aiming to address the origin of the soul but then Shawn pointed out:
“What I am most interested in, is how each soul arrives at each body, and what process of decision is behind who gets to be Brad Pitt and who gets to be the poor little girl with her legs chopped off.”
This question is not one specifically tied to substance dualism because a Christian materialist would be subject to basically the same question, albeit with a few tweaks:
“What I am most interested in, is how each person arrives in each body [i.e. the mother’s body], and what process of decision is behind who gets to live the life of a Brad Pitt and who gets to live the life of the poor little girl with her legs chopped off.”
So whatever the anthropology, we can still ask, as Shawn does, “How can your God morally justify “starting off” some souls [or persons] in perfect luxury and love, and others in opposite circumstances?”
A dualist aside
Dualism does enter into the picture at one point, albeit somewhat indirectly. Shawn’s understanding of dualism seems to view the process of what we might call “soul body attachment” to be rather arbitrary. On a whim he (God, not Shawn) decides to attach a Brad Pitt soul to this embryo and a Randal Rauser soul to that embryo. (Sorry about that body, but you can hardly blame me. And anyway I suppose I have as much a right to be ticked off as you. After all, you’re no runway model yourself chump.)
This might be a problem for some kinds of dualism, but most contemporary forms of Christian dualism do not view the soul body relation as an arbitrary attachment. Rather, this body (and specifically or essentially, this brain) is somehow connected essentially to this soul/mind. Thus when a particular sperm and egg unite to create a new biological organism the result is necessarily the soul/body person that comes to be and not possibly another. That takes off some of the arbitrary edge.
This is a big question. It is also a great question. So how shall we answer it?
First off, it is reasonable to say that God is God and thus has certain rights over his creatures that creatures do not have. Think of a person who raises dogs. Today three will be spayed, two neutered, while two others will chew on raw hide destined for the luxurious life of a stud. Is it wrong for this dog owner to do this? Few of us think the owner is being immoral because we recognize that the owner has certain rights over his dogs.
Is it plausible to think that God might have certain rights over his creatures, i.e. a kind of ownership, not unlike the kind of ownership a dog owner might have over his dogs? We may resent being compared to dogs, but if traditional definitions of God are anywhere near correct, then the chasm between human beings and dogs is miniscule compared to the chasm between human beings and God.
Creating a world
It is no mean feat to create a world with trillions of interacting organisms, many of them blessed (and occasionally cursed) with that bewildering capacity we call free will. But there is intrinsic value in creating a world like this and so God does.
Another analogy: you’re putting on a play and casting the actors. Inevitably not everyone can be a star. Some will only get bit parts. And other folk will have to be stage hands working the ropes. And others will have to usher or sell tickets at the box office. To make the analogy closer, think of the play as put on by grade 2 students where the various roles are assigned by the inscrutable Mrs. Kapakowski. Should the school not put on a play at all because some children will not get a starring role?
Let’s take our grade 2 analogy a little further. You see there is an offer on the table. Mrs. Kapakowski recognizes that not every child can be a star. But she has also benevolently offered all the children that excel in their duties in the play (straight from star to usher) a round trip ticket for a week in Disneyland following the final performance. Isn’t that some sort of compensation? Do you think that as the children spin in teacups with Mickey Mouse and take in the parade on Main Street at the end of a dreamlike day that some will still be grumbling because they had to work the ropes behind stage? On the contrary, such points of complaint will evaporate like a fleck of spittle on an August afternoon in Death Valley.
If the agonies of this world are inestimably worse than the lesser jobs of a grade 2 play, the joys of eternity are inestimably greater.