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You’re making too many assumptions. You’re laboring under the assumption that in either case, the mother considers herself a Muslim and that she would want to raise her child as one. If the mother doesn’t consider herself a Muslim (or, at least, not a terribly devout one) why would she raise her child as one?
I also don’t imagine an unborn child as anything, really, but if I can make my own assumption, it’s that a child who is raised in a loving, supportive environment will likely have better self esteem than a child who is not, regardless of how many parents or caregivers are involved.