This is news?
And I claim precedence on the phrase "just so story" for those things biologists have been spouting for decades.
The article does give the background here - there are multiple positions within evolutionary biology. All accept natural selection, of course, but the fine details matter too. In particular here the question is a decades long debate that Gould&Lewontin headed, saying that not all apparently-useful adaptations evolved, some are "spandrels" that arose for other reasons.
The article mentions other reasons to suspect that things that seem useful did not evolve, such as the surprising effect of drift in multicellular organisms (us) vs single-celled organisms. In the latter, selection affects each nucleotide of DNA. In the former, selection must be powerful enough to overcome noise, otherwise it is ineffective - which seems surprising, as this is averaged over many individuals over much time. The surprising thing is that this effect is, it turns out, non-linear.
Junk DNA is real, although it also serves as a broad canvas on which selection can subsequently act. Pervasive transcription doesn't mean pervasive genomic adaptation.
A significant number (perhaps even a majority) of biologists seem to hold views akin to a naive adaptationist outlook, which demonstrably leads them astray in their interpretation of data. The proportion of the educated public holding these views is even higher. Richard Dawkins has a lot to answer for.
Above all, a simplistic adaptationist view of evolution is not only inaccurate, ignoring the last half-century of developments in the field of population genetics, but also misses a lot of the (often subtle) detail that makes evolutionary biology so interesting.
The idea is basically that junk DNA contains a memory in shape of a distributed representation of the past of the organism and its environment, akin to how neural networks encode information. It basically provides a basis for fast adaptability by introducing noise into the gene expression and morphogenesis process so as to have more versatility and robustness to explore alternatives (very similar to dropout in neural networks).
90% of our genome is unconserved, meaning that it is not under selection. Most of this consists of dead viruses and mobile elements. Such DNA was present for its own purposes while it was active but is long since dead. A tiny proportion of this junk is later co-opted by the host organism.
The null hypothesis is that junk DNA is junk. It survives in the genomes of species with small effective population size because its selection coefficient is too small for it to be purged.
The alternative hypothesis you gave would need evidence to support it, otherwise it's another 'just so' story. Ask yourself, if this junk is beneficial for adaptation as you hypothesize, why don't bacteria have any? More broadly, why is the amount of junk DNA indirectly proportional to the effective population size (as the null hypothesis predicts)?