I'll take your word for it, because I've not looked directly at that question, just at tangential questions. I'm curious though to look into it further, so I will keep that in mind for whenever I have the chance!
And, to be sure, I do think it's an excellent point. The basic scenario being that a Neanderthal rapes a Cro-Magnon, who returns to the cave and later bears the child, and raises the child not realizing it's a hybrid, having made no connection between the rape and the child.
I very indirectly addressed this in two ways. Above, where I mention that in order for the Neanderthal genes to persist we must assume that the human community survives, the point I was getting at is how did the Neanderthal rape the human woman in the first place? In general, the community would seek to protect its females and if Neanderthals were wont to rape human females to begin with (a questionable proposition in my view) then that's all the more reason for them to be protected by the community.
Secondly, the hybrid would presumably look deformed, and we know that most premodern cultures practiced infanticide of deformed infants.
So, we have two big hurdles, even without the cognitive connection: (A) the Cro-Magnon woman has to be unprotected and thus subject to rape by Neanderthal; and (B) the presumably deformed child has to not be killed. And actually, we have a third hurdle: (C) Neanderthal males have to want to rape human females.
And of course we know nothing at all about Neanderthal sexual behavior, and never will. The whole notion of sex with a human female might've been unthinkable to them.
I am not saying that it never happened not once even a single time (although it's certainly possible in my view) but if it did happen it must've been exceptionally rare and ultimately inconsequential to the gene pool, IMHO.