This really is not as earth-shaking as the headline would have you believe.
Cells that have a limited quantity of mRNA processing enzymes end up breaking down a greater quantity of mRNA. In this case, the control is being exerted at the level of synthesis of the mRNA processing enzymes, not at the level of mRNA. The fact that stop codons are embedded in the introns is not new knowledge; it is a fail-safe mechanism ensuring that the cell does not expend a lot of energy trying to make proteins from non-processed mRNAs.
What this article is really saying is that cells are horribly inefficient at the molecular level. But we already knew that. (Well, at least, those of us who have spent enough time studying biochemistry to get a PhD in the subject know that.)
Junk DNA is still junk DNA.