“junk DNA” was supposed to be, along with mutations thereof,
the source of new structures and functionality of the next stage of evolved critters.
It was also used as the “get around” for irreducible complexity.
Seeing as irreducible complexity is solely a manuifactured term used to push ID, I find no reason why anyone needs to figure out a way to “get around” it.
When I learned of junk DNA, there were no real theories of function. There were guesses about past function, but nothing more was said of it.