As I mentioned, I don't have the time for a serious rebuttal, which would take many hours. But I'll give you an illustration of how a more comprehensive rebuttal would be structured. For further thoughts on the nature (if not the details) of the problem, please refer to the chapter in Massimo Pigluicci's Nonsense on Stilts (https://www.amazon.com/Nonsense-Stilts-Massimo-Pigliucci/dp/022649599X) on "Almost Science", with special (but not exclusive) attention to the nature of the problems listed in the section on evolutionary psychology. In a similar vein, most of the concerns about the nature of the problems (though not necessarily the details) with evolutionary psychology discussed by David Buller in Adapting Minds (or the SciAm article: https://www.scientificamerican.com/article/psyching-out-evolutionary/). Let me repeat: I am not (mostly) saying that the exact same criticisms apply because those depend on details which are different. I am saying that the weaknesses in the case that you (and the people you cite) are mostly of a similar nature.
In terms of scope, I am going to address the methodological problems with the claim, "Human society was prehistorically egalitarian, not a dominance hierarchy, and this demonstrates that men are not intrinsically prone to violence."
1. Inadequate conception of "Human Nature"
You don't need to do any anthropology at all, only look around at human societies today, to recognize that humans are capable of adjusting to a wide range of different social conditions, both at the level of societies and even from day-to-day. Furthermore, we have very strong evidence from people being raised as children in different cultures that it is mostly if not completely behavioral plasticity (at least during maturation) rather than genetic variation that explains this difference.
Given this, for any behavior in question, the entire spectrum from "this is intrinsic and insensitive to cultural pressures" (like eyeblink) through to "this is extremely unnatural but with lifelong training can sometimes be achieved" (like celibacy of monks) needs to be considered.
Because of this immense plasticity, for any question like "do men have a propensity to violence", we cannot simply observe societies with non-violent men and conclude "no". All that disproves is that "male violence is intrinsic and insensitive to cultural pressures". Rather, if one is arguing against a propensity, one at least needs to show convincingly that the social effort required to entrain one behavior is considerably larger than the social effort required to entrain the alternative: this would argue that people have a propensity to the second relative to the first.
You could have a time machine and an army of a million anthropologists and conduct a comprehensive global survey of all hunter-gatherer tribes 100,000 years ago and if you didn't explicitly measure how much effort, if any, is needed to be applied to raise non-violent men, then you wouldn't be answering the question. It could just be that under those conditions, taming the violence of men was extremely important and so every successful tribal culture makes the effort to do it enough to overcome the propensity to a sufficient degree.
2. Inadequate historical knowledge to support claims
Pre-agricultural cultures have tended to leave few traces of their activities and study of those traces is adequate to have cause to doubt a narrative of pervasive violence but not to establish a pervasive peace.
Ferguson (from your link) talking about the beginnings of war: "“Most of sub-Saharan Africa has negligible archaeological excavation, so who knows?” he said. “New Guinea: also almost no evidence, though northern Australia seems to have potentially lethal group clashes (among hunter-gatherers) as early as 4000 BC, and continuing thereafter.”"
I found and linked two instances of skeletons with multiple violent injuries from way before the time period Ferguson was talking about. Set that--given the very incomplete historical record--against "For example, a researcher examined 209 Middle and Upper Paleolithic remains, including Neanderthals, from southern France and found five fractures. That research concluded “the absence of a single parry fracture or wound to the side of the head in my sample seems to belie the previously held notions in the literature of bestial behavior and violence for this time period.”" and you have...nothing remotely conclusive except that rampant violence was not ubiquitous.
The difficulty of interpreting what data we have is compounded yet further by us not having any reason to believe that when we find skeletons, we get a complete or representative sample. A change in the nature of burial and/or how the dead are dealt with can be misinterpreted as a change in conditions.
The evidence is more than adequate to disprove a narrative of unending violent savagery. But it is not adequate to set narrow bounds on the degree of violence, and while Ferguson seems willing to concede the point (at least in places) in the interview, you mostly don't.
3. Inattention to the timescale and nature of evolutionary pressure
Our nearest relatives that have social organization all have dominance hierarchies and substantial levels of violence. According to Ferguson, widespread violence of the "war" type became widespread from 12,000 to 6,000 years ago in the places he is confident enough to make a call on.
However, 6,000 years (~300 generations) is plenty of time for any allelic variants that give at least a modest survival advantage to go to fixation. And 6 million years (time to common ancestor) is not nearly enough time for random drift to remove behaviors no longer under selection, nor for new mutations to arise and those to be driven to fixation.
Therefore, given that genes are what determine what is intrinsic about behavior (under most terminology), any historical evidence would need to be supplemented by genetic evidence, for instance, that appropriate regions of the genome (those under sexually dimorphic control and relevant to aggressive behavior) were under positive or negative selection for the requisite period of time where there is evidence that violence was low and social organization was egalitarian, but that there has not been significant selection since.
Given that we don't know how genetic variants contribute to violence, let alone those under sexually dimorphic control, you can't really get at this at all. But it is essential to be able to establish the claim from historical records. Thus, methodology that doesn't include genetic evidence is ill-suited to make conclusions about what is natural.
Put simply: if you observe A, B, A', and you argue that B is relevant, you have to show that the adjustment from A to B happened, but the adjustment from B to A' did not.
4. Lesser but still significant methodological and rhetorical problems
These are mostly with your answers, not the literature (that I've seen). This is not an exhaustive list.
(a) Excusing contrary evidence rather than adjusting the strength of claims or adjusting the model (c.f. not addressing the paper on Pacific NW indigenous tribes; "Even when we get to the point where some indigenous cultures have a chief (Polynesians), or women don’t have nearly the power that men do (Australian Aboriginals), there are still strong elements of egalitarianism..."" with no quantitative assessment of the degree of egalitarianism in modern societies compared to the others to show that the sign is even in the direction you suggest.)
(b) Definitions shifting to suit the argument rather than being stable and arguments made to definitions (c.f. "unrestrained aggression (the last category in Figure 23.1) is exceedingly rare among mammals" vs "when we encourage violence and the threat of violence as a display of true masculinity", jumping hither and thither over vastly different levels of violence without clearly establishing what claim is being supported, e.g.: Let's consider the idea that unrestrained aggression (defined as so-and-so) is an innate and unavoidable male trait.)
(c) Lack of consideration of alternative hypotheses regarding violence, e.g. that there is a propensity to be violent, but the target doesn't matter; so hunters can express the propensity there, but if you fail to have something to hunt the propensity isn't satisfied.
(d) Failure to use extant high-reliability cultural examples that suffice to make the same point. For instance, just point at Japan or Norway.
Summary
Overall, I think there is ample, abundant evidence to cast a great deal of doubt on a simplistic never-well-supported idea that prehistoric human history contained a great deal of interpersonal violence.
However, there is not adequate evidence to support a new non-hierarchical egalitarian model, and there certainly isn't the evidence needed to claim that historical non-hierarchical egalitarian human lifestyle disproves that men have an innate propensity to violence (relative to women).
Furthermore, the idea that this is the "scientific" view is a denigration of what it means for something to be scientific, as it is not widely supported by evidence with many alternatives examined and rejected, but rather one plausible account that isn't presently too egregiously contradicted by evidence. The scientific view is necessarily vastly more tentative given the quality of the evidence.
Again, this doesn't mean that I think that some other hypothesis fits the data far better. Rather, it is that the confidence we can have in any of this is overstated, and the confident overstatement itself is bad because it lends itself to ideological thinking rather than responsiveness to additional evidence.