Mr Mabbutt said the photos, which a former partner of Holdom's said she found on an SD card from his phone, were the most important piece of evidence in the crown's "large, complex and circumstantial case".
Ms Engel argued "the evidence, including photographing her body in situ, as a trophy of sorts, was all indicative of an intention to kill" his girlfriend Ms Pearce-Stevenson.
Her remains were found in the forest in 2010 but were not identified for five years until after the discovery of Khandalyce's remains some 1200km away in 2015.
They were located with a suitcase on the side of the Karoonda Highway, west of Wynarka, in SA.
Holdom and Ms Pearce-Stevenson were seen to argue while staying with people at Charnwood in the ACT on December 14, 2008, before they drove off in her car.
The housemates said Holdom returned alone after being gone for about 14 to 17 hours, the magistrate said.
Ms Engel alleged he cleaned her car, sold it and obtained another car which he drove to Wagga Wagga, purchasing duct tape and a dishcloth, before checking into a motel with a child.
But he was alone when seen the next day before he drove on to South Australia.
An elderberry towel, having the same batch number as those used at the motel, was found with other items near Khandalyce's remains.
"The location where the suitcase was found several years later was entirely consistent with the route of travel he took," the magistrate said.
Ms Engel said Holdom used Ms Pearce-Stevenson's credit card for years after her death, during which time numerous benefit payments continued and $71,770 was debited from her account.
He also was allegedly involved in sending messages from her phone to her mother to curb police investigations into the pair's disappearances.
The case was listed for arraignment in the Supreme Court on October 6.