Rather, it tends to undercut the very basis of comparative molecular clocks on the time scales in questions. The underlying chemistry of RNA and DNA is independent of the environment; so the base rate of changes to the allele within each new generation can't change.
Which then means the previously alleged "Because it's SCIENCE!"TM (looks down over glasses at the questioner) description of the specific environmental changes to produce the observed changes in the allele between one species and the next,...all go out the window.
That's a broad brush, and there are significant additional considerations, but it's good enough to start with.
That's significant - but hardly the undercutting of naturalism that the article insinuates.