You might be right, but you are still left with little but idle conjecture to support the notion that Neanderthals were assimilated by Cro-Magnon.
And as for myself, I'll essentially repost the comment I made on this topic yesterday: Any interbreeding was probably minimal at best. So, I am not saying that it never happened at all, just that it almost certainly didn't happen to any degree of consequence.
If you take any small subset of human population, you will find distinctive aspects of the DNA of that subset. That is a direct consequence of the fact that sequence space is astronomically larger than whole populations, over the whole course of history. Which is the same fact used to recognize individuals by their DNA.
If you then ask, is that exact same subset of distinctive features found in some other separate population, the answer is overwhelmingly likely to be "no". But not because the other, separate population is a homogeneous pool in all respects, distinct from a likewise homogeneous pool that you choose as your starting point, and noticed the distinctive features of. Instead, any sizeable subset of the broader pop you compare it to, will also have distinctive features - just not *those* distinctive features.
Species are not points in sequence space but clouds. They agree on gobs and disagree on tiny subsets. N. and H.S. were supposedly unified at 500ky based on the degree of simularity noticed in their sequences. Which is itself a very rough analysis that assumes more pointlikeness (common descent from some X? But X is a cloud, not a single sequence) in the past than there was. What it really tells us is that people on different continents for 100ky periods had limited gene flow. Duh.
There is no reason to believe the markers used to tell N. from H. have any selective effect whatever, or matter for anything. They are fingerprint whorls, effectively. All they tell us is subpop A was not subpop B, which we knew by the operation "subset", and ordinary statistics.
The actual argument used in the paper linked, however, is transparently absurd. It claims any diffusion event will leave the diffusee vastly overprevalent in the subsequence pop. Without anything motivating the implied assymmetry.
It is clear to me what they did wrong. They talk about "logistic population" effects as an amplifier, but logistic under the assumption of a higher carry cap locally, is exponential in all but name. They assume that the pop of the crossover is exponentially expanding. And then they have only front crossover, no actual movement. Which damps any long range gene flow and only allows the supposedly so much more rapidly expanding bit to spread.
Such one sided exponentials litter models with specious results. If this happened we'd see it all the time in all other similar cases, but we don't. Assimilated subpops are not assured 95% genetic representation in larger pops assimiliating them. Duh. Instead, larger a few generations later, plus drift, form a strong attractive force for conservation of the most common alleles.
Until I see better evidence, I remain convinced that N. are completely made up, simple a trivially different subgroup of humans with modestly different hat sizes, being chased around by molehill mountaineers.