I guess Mundus isn't beyond impregnating a woman with stolen demon spunk either, of course. I agree that it doesn't give Nero enough time to grow up (this is why I generally discount theories that Vergil is Nero's father to begin with). Since Nero clearly ages normally and Trish has looked like an adult since inception, they must have had different origins.
I wouldn't be surprised if Mundus had his own worshippers, just like the Order, in which case one of them may have given themselves willingly to bear Vergil's son, keeping him as leverage. After Mundus's defeat, this woman may have given up Nero willingly, but the Order may have in fact kidnapped Nero and lied about the orphanage.
Still, none of these ideas really clicks with me. They all have massive problems even compared to existing theories that I also don't find convincing.