The Mystery of Skulls

From the oldest archaeological finds it is important to note that the first bipedal hominids were walking on two legs BEFORE they had enlarged brains and "modern-looking" encephalization. This alone says a lot about people today as well. All one has to do is to stay still in a spot to observe people wandering and walking about to and fro to fulfill their daily tasks and objectives that they personally bestow upon themselves consciously and subconsciously. Most of that motivation though probably has its origins in subconscious trickery acting on the conscious mind but that is a topic for another time that delves into free will.

One should also take notice of how people with more "modern-looking" skulls are not always the 'brightest' or the most cognizant even when compared against their more archaic yet contemporary bretheren. This is probably due to a particular single gene or set of genes that activates or deactivates higher cognition. Therefore they could easily be imbued with the necessary essential tools and abilities but not have them "turned on" for use. Putting intelligence aside there is also the idea that the more modern an individual's skull is the less emotionally susceptible and reactive they will be to percievable threatening stimuli thus making one more peaceful, cooperative, understanding, compliant, and less aggressive in order to seek out or instigate conflict. This feature too once again could be present and available for use intrinsically but the necessary genetic triggers would be absent or "turned off" to prevent active usage. I personally can't give much credence to that idea though. One only has to look to the example of the more peaceful matriarchal bonobos and the more warlike patriarchal chimpanzees to take note of the fact that both of those apes have the same archaic skulls despite their distinct societal differences.

Finally it must also be said and considered that the shape and/or encephalization quotient of the skull might not have any significant bearing or outcome whatsoever on the individual. Many societies, most notably and famously in the pre-Columbian world, once commonly practiced artificial cranial deformation such as the elongation of the skull. It is purportedly said in certain chronicles that whatever individuals that had their skulls intentionally deformed suffered no apparent or significant mental impairments and were "normal". It should also be noted that in some case example societies it was only the elites that had the exclusive rights to practice artificial cranial deformation in order to differentiate themselves from the commoners they ruled over. One can only conclude that such individuals belonging to the elite would not be able to control and manipulate the masses if they were mentally impaired in any way or of sub-standard intelligence.

"Curiously, Dingwall [19] maintains that there is no solid evidence accounting for the diminishing of the mental faculties of one who is deformed, even though others have raised the issue [25]. Additionally, Gerszten’s  [14] study of over 400 pre-Columbian skulls shows no apparent difference between the cranial capacities of the deformed and the undeformed skulls, lending support to the view that the brain is unharmed and that normal brain function is unaffected by the deforming procedure. It is noteworthy that ACD is an alteration in direction of growth not magnitude of dimensions [26]. Furthermore, contemporary studies [9] suggest that there is most likely neither injury to the brain nor impairment of the mind in the case of ACD. It is worthwhile to consider that the artificially deformed individual’s mental functions or abilities might actually be augmented in some manner."

https://www.omicsonline.org/artificial-cranial-deformation-potential-implications-for-affected-brai-function-antp.1000107.pdf

"Hoshower et al. (1995) reported that the Inca used cranial deformation to mark the elite and as a way of distinguishing themselves from the citizens of their empire (see also Romero-Vargas  et al., 2010).  In the same way, Incas homogenised the type of deformation in each group to better identify the different members of  their empire (de las  Casas,  1892,  p. 594-595  apud  Torres-Rouff and Yablonsky, 2005).  For  Torres-Rouff  and Yablonsky (2005), this example offers some documentation that can be used  in order to understand what can be found in the archaeological record of other groups. Although the reasons for the adoption of the practice of cranial deformation vary from group to group (Dingwall, 1931;  Garrett, 1988),  it is well known  that most of the groups considered this practice as a sign of high status, and frequently slaves were not allowed to practice it. For  example, Nagaoka  et  al.  (2012)  describe the skeletal remains of a female individual found in a cemetery from the northern highlands of Peru dated from the Formative period (2500-1 BC). The individual presented artificial cranial deformation and a high stature, being buried with a pair of gold earplugs, a pair of  gold earrings, and shell objects including a necklace and leg ornaments. The characteristics of the burial were interpreted as a possible evidence for social stratification in the Formative period."

http://www.scielo.br/pdf/bgoeldi/v9n1/02.pdf

All of this though that has been aforementioned is of course only relevant if the world is real.

If the world is fake, like in the case example idea of it being an "ancestor simulation" of some sort, then these cranial differences could merely be ways to serve as "markers" of some sort. They could also mean nothing and it could merely come down to "avatar" design and customization. 

Suffice to say it should also be obvious as to why these cranial differences would not have much bearing on individuals if the world is indeed fake.