When a conquerer rapes a woman and she bears the child and raises it the child is in the conquered community. The two communities get mixed, but over in the conquered community.
If a Cro-Magnon raped a Neanderthal and she had a child over in the Neanderthal community that is irrelevant to the issue at hand. Because the Neanderthal communities all eventually went extinct, so any intermixed genes also went extinct.
So, in order for the the genes to persist, it would have to be a Neanderthal that raped a Cro-Magnon woman, and then the woman would have to return to the Cro-Magnon community and birth a product of that rape and also raise the product of that rape.
This is all presumed for the simple reason that we do not find evidence of mixed communities. If we did, then this whole debate would be moot...
Well, perhaps they were so anti-social (like animals) or unskilled that they couldn't be kept. This is what I mean by stronger differences than simply "social norms" as we apply them to human groupings.