Again, and I can't emphasize this enough, this is not my area of study and seems like you have better handling of the subject. But when I read his quote, this part sticks out to me:

much of the exquisite control over these proteins is held offstage, nested within the noncoding junk.

Additionally, the article calls into question the role of code and protein production as the only role for DNA.

Still other noncoding stretches may be buffers against precipitous change, serving rather as flak jackets to absorb the impact of viruses and other genetic interlopers that infiltrate an animal's chromosomes. Without all the extra padding to absorb the blows, viruses or the bizarre genetic sequences that hop and skip from one part of the chromosome to another -- mysterious genetic elements called transposons or jumping genes -- might land smack in the middle of a crucial gene, disrupting its performance.

So there maybe stretches of DNA that don't participate in protein construction, but still has a role. So I question I idea of centering one type function over another.

But it doesn't do that instantly and it does it for good reason, eyes and the sections of the brain using them require energy and are vulnerable to infection so in situations where they don't provide an advantage they increase the likelihood of death before breeding thus giving any offspring born with less energy devoted to eyes has a small advantage which over s very long time results in them being selected away.

So unless the creatures reach a perfect form for their environment then they'll always be in the process of changing and have some of the old junk in there. Also if the formerly useful part doesn't make any real difference to survivability there's no force driving it to be selected away from, it might eventually be removed by lots of pure chance events but that's going to take a huge amount of generations meaning the middle time where there's junk not yet removed us going to be very long