I'm thinking this junk DNA gets used in the embryo stage of life to follow the evolutionary processes that occurred from a one celled organism to the present multi celled species. I'm thinking encoded in our junk DNA is our entire evolutionary history and these get turned on during different segments of our progression after fertilization to gradually built the entire species to its present mature form.
https://www.nytimes.com/2015/03/08/magazine/is-most-of-our-dna-garbage.html
But in the past few years, the tide has shifted within the field. Recent studies have revealed a wealth of new pieces of noncoding DNA that do seem to be as important to our survival as our more familiar genes. Many of them may encode molecules that help guide our development from a fertilized egg to a healthy adult, for example. If these pieces of noncoding DNA become damaged, we may suffer devastating consequences like brain damage or cancer, depending on what pieces are affected. Large-scale surveys of the genome have led a number of researchers to expect that the human genome will turn out to be even more full of activity than previously thought.