I agree there are more questions to explore here but at the end of the day it is pretty clear that the gene duplication and divergence mechanism is limited as an explanation for new functional sequences. There are papers discussing the time to fixation of gain of function mutations we have discussed here. I will post them in a private message if you like.
If we look at the number of different genes between classes of vertebrates it looks like multiple origin events. I know John believes that he has confirmed a single origin event thorough the pattern of phylogenetic nested hierarchies. I think his conclusion can at best be tentative until the gene and chromosome differences can be mechanistically explained.