I actually don't think they can, except on TV! Maybe someone who knows more about forensics can reply but I am quite sure that forensic science can only provide approximate ages from skeletal remains, as well as only very approximate time of death once a body is entirely degraded to skeleton. Children develop at different stages, height varies etc.
On another note, I used to read a lawyer's blog that provided info on whether aspects of Law and Order:SVU were "realistic". She commented about DNA a number of times--not only does creating the DNA profile take quite some time, it then takes weeks annd months again to search for a random match. Searching through the DNA database takes a long time, and while assisted by a computer, it is a person who does the matching and comparison, one by one to each possible match. There is no real-life computer program in the world that spits out an answer in a day. So I also feel that comments that LE should have known beforehand to compare DNA from the two cases are unfair--it seems that they only just got the DNA profile a very short time before they got the lead on Khandalyce, and by identifying Khandalyce they knew they could focus a comparison on any unidentified remains of a young female, because only by identifying Khandalyce as the victim is there a strong indication that her mother was also a victim. Prior to the identification of Khandalyce, the line of inquiry that she had a mother murdered as well was only as likely or unlikely as any other scenario, and in my opinion did not deserve more attention than other lines of enquiry.
In my opinion, the strategies used by LE to identify Khandalyce worked. They asked the public to think about little girls who would have been aged between 2-4 years 2008 - 2014, and to ask themselves where those little girls are now--a relative of Khandalyce clearly thought about this prompting their call to Crimestoppers. LE regularly displayed and brought media attention to the quilt--another relative found and provided a photo of Khandalyce with the quilt. They were able to compare an item of Khandalyce's clothing to another picture sourced from a friend. They found Khandalyce on a list of names of children dropped off the immunisation register. And finally having a DNA profile they could use, they matched it to Khandalyce. I'm sure that a lot of time was also wasted on enquiries that led nowhere, but that is the case for most investigations like this.