So you’re assuming the truth of something objectively false in order to free up your scientific research? That seems counterproductive. Junk DNA isn’t an assumption, as you seem to think. It’s not DNA whose function we don’t know, as many people unacquainted with the science seem to think. There is positive evidence for lack of function, which you are choosing to look past. That isn’t how science ought to work.
Small amounts, perhaps. Essentially, it might explain the sizes of a few introns. For most introns, the c-value paradox in miniature — intron lengths varying dramatically between closely related species — kills off the general case. And of course it’s completely irrelevant for non-genic sequences.
There is no puzzle unless you make the unwarranted assumption that all DNA is functional. The computer code analogy is a blind alley.