Great question, I had answered something similar a couple of years ago which I will rephrase and adapt to this. The piles of skulls are not a Cambodian custom, in fact it could be said that these memorials are the opposite of traditional burial rituals. It was not aimed at disposing bodies, and the symbolic nature of these ‘piles of skulls’, was more political than anything else.

It is helpful to first outline the political context of Cambodia following the expulsion of the Democratic Kampuchea regime (DK). In particular, aspects relating to the continuation of a Marxist-Leninist political system. Following the Vietnamese led invasion of DK, the People’s Republic of Kampuchea was established (PRK). Many of its leading officials were former Khmer Rouge who had defected in the latter stages of the regime, and naturally it was a state that had certain important functions or policies directly in line with Vietnamese interests.

This local context must also be viewed against the international one. The invasion of DK was argued by certain governments to have been illegal, and the remaining Khmer Rouge were supported, sometimes in a clandestine way, by states with an interest in essentially causing a headache for Vietnam and its Soviet benefactor.

The Vietnamese backed regime was faced with a problem. The PRK officials needed to distance themselves from the Khmer Rouge, but without disavowing one-party socialist rule. This was done by demonising just the very top Khmer Rouge party members: Pol Pot, Ieng Sary were generally put forward. Historian David Chandler says that the ‘genocidal Pol Pot-Ieng Sary clique’ was blamed for the catastrophe that occurred between 1975-79, as opposed to ‘the extreme but recognizably socialist policies of the Communist Party of Kampuchea’. The two were tried for genocide in absentia in 1979 and condemned to death. Soon after this, the ‘Tuol Sleng Genocide Museum’ was opened in Phnom Penh on the former grounds of the S-21 interrogation centre.

A large and elaborate sculpture depicting the map of Cambodia, filled in with skulls and a river of blood (made from the remains of those buried at the nearby execution site) was on display at the museum until 2002. The museum was originally directed by former Vietnamese Colonel Mai Lam, who also worked on the Vietnam War atrocity museum. There was a deliberate attempt to associate the Khmer Rouge with fascism, Pol Pot with Hitler and S-21 with Auschwitz. All of this was aimed at denying the Khmer Rouge their socialist credentials and paint the leadership as genocidal criminals, without condemning the entire movement and therefore many of those currently in PRK leadership positions. It also sent a clear message to the rest of the world that the Vietnamese invasion had toppled a regime that had been systematically murdering hundred and thousands of its population (the current figures are still not exact but sit somewhere around 2 million dead with perhaps up to half of that number being the result of execution).

The Tuol Sleng Genocide Museum was not the only attempt at exhibiting these atrocities to the world or to Cambodians. The PRK also began the process of exhuming the mass graves around the country. People in villages and towns were instructed to dig up any nearby ‘killing fields’ and arrange the bones and skulls as seen here http://d.dccam.org/Archives/Photographs/Provincial_Photo-Archive/Svay%20Rieng/slides/Bone41.html. It would be too cynical to say that this was a directive to only prove a political point. That is not the case, but it was part of the process of the new Cambodian government (essentially under the control of Cambodia’s “hereditary enemy”, the Vietnamese) to have a visceral and shocking reminder of what had preceded them on show for the Cambodian population and the world. The arrangement of the skulls and bones was sometimes quite orderly, sometimes not, which can also be seen in the difference between the previous picture and this one http://d.dccam.org/Archives/Photographs/Provincial_Photo-Archive/Svay%20Rieng/slides/Massgrave50.html . There was, to my knowledge, no special meaning behind the arrangement and it may have been a prudent way of counting the number of victims at a given site or indeed presenting them in a way that was easily captured with photography or the imagination. It is a shocking and brutal image which leaves an ongoing impression, both for young and old Cambodians and what would eventually become a tourist attraction. The images of ‘piles of skulls’ are firmly associated with the western conception of Cambodia and the callousness of the Khmer Rouge regime.

In many ways the ‘intent’ of these images served the purpose outlined above. It is hard to escape the power of them, hard not to be utterly devastated by what they represent, while I have visited these sites and viewed these images many times over the last decade, the emotional impact remains. It should be noted too that ‘exposing’ these bodies to a wide audience also served to ‘prove’ the regime had been conducting mass killings, some observers abroad – as well as the Khmer Rouge – had been denying this.

That being said, it has also been proposed by different groups that these ossuaries are contrary to traditional Cambodian/Theravada beliefs. To not properly bury their dead or cremate them is thought to prevent the spirits of the dead from finding peace. Not being Khmer myself, I will not comment much further on that but I have seen prominent ‘survivors’, like S-21 inmate Chum Mey, contend that the memorial stupa at a place like Cheoung Ek is a useful reminder rather than a sacrilegious display. So there may not be a consensus there, but the idea that they were originally set up by the Vietnamese (who share different beliefs) as a political message, but still remain visible today, is thought to be problematic by others.