Oh, certainly, you reduce the explanatory power of an explanation, you lower the probability of the explanation being true.

But, well, "parasite DNA" at the fundamental level is assuming Darwinian mutation-and-selection happens among transposons. Which seems quite plausible on its own, even after this, especially since retroviruses can be treated as a special class of retrotransposons.

And now that I'm actually looking at the paper instead of the news, it's not clear how much of this stuff is "functional" because it actually does something like regulation of expression, and how much is "functional" because it's biologically active "parasite DNA".

Mostly, I'd classify this as another case of "no, really, skip the science news, and read settled science instead."