The article he linked did not mention code skipping or even suggest the concept.
Here's what the article says:
The idea that genes previously regarded as 'vertebrate innovations' may have evolved before vertebrates did isn't new. Alejandro Sánchez Alvarado, a developmental biologist at the University of Utah, previously found genes in the flatworm Schmidtea mediterranea that were thought to have evolved in vertebrates.
But the idea that some animals may discard genes as they become more sophisticated is still controversial. "We won't really know until we have more worm and insect genomes to compare,"...
An article posted yesterday described a deep sea creature with absolute no "junk" DNA. Surely this answers the question about whether unneeded genes can be discarded.
I know, I did read it after all ;-)
It's just that he brings this "code skipping" up again and again (had it already addressed on two other threads).
What he perceives as "code skipping" is just an artefact of his model which presumes a linear progression from A to B to C.
The more likely scenario is where B loses this particular gene only after population C split off.