So this is kind of a complex question and I have done my best to answer it by referring to the history of memorial representations in Cambodia following the Khmer Rouge being toppled in 1979. To summarise, it was a politicised image - and one that has been built upon by a succession of journalists and now foreign tourists. It is also a visually striking image and one utilised to inform in a very base/human way the almost unfathomable suffering of the Democratic Kampuchea period.

The image of the skull, or skulls - or piles of skulls - had been adopted by Mai Lam, who was a Vietnamese Colonel fluent in Khmer and had extensive experience in legal studies and museology, from the earliest points after the S-21 security centre was turned into the 'tuol sleng museum of genocidal crimes'. A large painting of a map of Cambodia, filled with skulls, and rivers of blood was on display until 2002, similar paintings hang in the museum today. The crimes of the Khmer Rouge were politicised by the new government in Cambodia which was essentially under Vietnamese suzerainty. Without going into too much detail - there is a reason that the museum at S-21 was made to be very reminiscent of museums associated with Nazi concentration camps. The idea of the exhibit was to (according to David Chandler) 'deny the the leaders of the CPK (communist party of kampuchea) any socialist credentials and encourage viewers to make connections between the DK regime (democratic Kampuchea) and Tuol Sleng on the one hand and Nazi Germany and Auschwitz on the other'. Remember at this time the communist Vietnamese were seen in some circles to have invaded Cambodia illegitimately (The US and China managed to keep the KR in their seat at the UN). The PRK government in Cambodia based its legitimacy on the fact that it had toppled a 'genocidal regime' (rather than a callous, radically marxist one), however it was in no position to condemn the entire movement as so many prominent figures in this new government were former Khmer Rouge Cadre until they had defected to Vietnam in 1977 and 1978.

So you have a situation wherein the new government is trying its hardest to be highly explicit in its condemnation of the very top leaders of the Khmer Rouge, they were tried in absentia and sentenced to death in 1979 in the first tribunal to accuse the 'Pol Pot Ieng Sary Clique' of genocide (the second is ongoing). In evidencing these accusations it became prudent to highlight to the world what the worst aspects of the Khmer Rouge period were - and one of the most straightforward ways of doing this would be to expose and excavate the hundreds of thousands of dead bodies which had been victims of execution during the regime. The so called 'killing fields' were dug up, and photographed. It is way too cynical to say that this was only done to prove a political point - obviously there is an historical and human element to digging up this tragedy - but when you visit places like Tuol Sleng, or its accompanying murder site Cheoung Ek (or the Killing Caves at Phnom Sampeau that you seem to be referencing in your question), the very explicit exhibits of bones and skulls stacked up behind glass is meant to viscerally remind the onlooker of the tragedy that befell Cambodia (and maybe who stopped it as well).

I'm afraid I cannot right now give you an accurate answer as to when these images of skull piles began to be a prominent image associated with Cambodia. The Toul Sleng museum opened in 1979 (the blood and hair of prisoners was still visible on the floor to these early visitors) and international visitors were the only ones allowed for around a year. In this time period John Pilger published his influential documentary 'Cambodia Year Zero' but while there are a few shots of a broken skull there were no piles of bones depicted. Similarly in 1984 'the killing fields' by Roland Joffe was released to much acclaim and the 'idea' of Cambodia and the devastation of the Khmer Rouge was solidified in the western consciousness, one scene depicts a vast waterlogged bone field. I don't have evidence for this but I would assume in the mid 1980s once the memorial stupa was erected in Cheoung Ek (the large column containing thousands of skulls behind glass) the image may have become more prominent. As this 'killing field' and the museum at S-21 are basically locked in for any tourist going to Cambodia it would make sense for the striking images and photos of skulls to be disseminated into the wider 'western image' of Cambodia from this point on. In the mid 90's when the UN transitional peace process occurred there was a wider interest in Cambodia again as it was seen as 'opening up' following the Cold War. Around this time Ben Kiernan publishes the 'Pol Pot Regime', the cover of which is just a photo of skulls excavated with blindfolds still attached. There is a long tradition of books on the subject employing this kind of imagery - and for good reason, it is a striking image from a sales point of view.

As for why the skulls are often arranged in this particular way? I am unaware if there is any cultural significance of the glass, or the arrangement of the skulls in this imposing manner. I have seen many photos of other mass graves excavations around the country and the skulls are often stacked or laid out, it may be a helpful way to account for the number of dead in any given killing site. As for the more 'elaborate' installations near the capital, Mai Lam had also worked on the Vietnam War atrocity museum where the idea is to really move an audience or visitor. I would presume that the arrangement of the skulls is done to primarily shock the viewer, both young and old Cambodians and maybe even more importantly the international visitor. It is actually a fairly alien custom to the Khmer, who are around 92% Theravada Buddhist, to not properly bury their dead or cremate them. It is thought the dead may not find peace if they are not properly buried. As I alluded to previously - these kinds of ossuary have two primary purposes: to shock and remind people of the Khmer Rouge period, and in doing so legitimise the government that toppled the callous regime responsible for these atrocities - and the second being one more traditionally associated with memorial.

A more simple answer may be that people are fascinated with these kinds of morbid tourist attractions - I would guarantee that 4/5 people you know who have visited Cambodia have a photo with them next to one of the exhibits of skulls at S-21 or Cheoung Ek. At the National Gallery of Victoria a recent exhibit by Ron Mueck entitled "MASS" - gigantic white skulls spread throughout a room - is directly influenced by exhibits like those in Cambodia or Rwanda. For many, myself included, seeing the nightmare of the Khmer Rouge regime represented in fields of bones and skulls is an enduring and powerful image, it makes sense that it is so often associated in the western consciousness with Cambodia.

A good secondary source to consult for this is David Chandler's "Voices From S-21: Terror and History in Pol Pot's Secret Prison", as well as articles like Madness and Mayhem: The Aesthetics of Dark Tourism by Collette Copeland.