you shouldn't allow the idea that evolution only stems from changes in genes the way you define this to stymie your thinking - Ruby
Evolution does "only stem from changes in genes". If the genome doesn't change no evolution has taken place.
As Shepherdless said I didn't link to any articles in my OP but the evolution of pigeons has nothing at all to do with phenotypic plasticity.
Put simply, some insects have genomes that allow alternative body plans to be built depending on environmental factors. It's a bit like having plans for a modular building where parts can be selected and modified depending on needs.
To illustrate - every cell in your body has all of the genes required to make an eye. These genes are only switched on in two locations. Geneticists have switched them on in multiple locations in fruit flies with interesting results.
This is not evolution. Phenotypic plasticity is about development within a specific generation. Evolution is about changes in the genome between generations. However phenotypic plasticity may result in a selective pressure that drives evolution in a particular direction. For example let's say phenotypic plasticity builds a version of an insect body that favours a nocturnal lifestyle. This may result in other evolutionary changes over many generations. Colour optic genes may be lost for example.
There is speculation in the article SBF linked that there may be a way for phenotypic plasticity to alter the genome more directly.
There is no basis for SBF's assertions about "Dawkins' strident materialism and atheism". If other mechanisms of evolution are discovered the process will still be about chemical nuts and bolts. To bring atheism into the conversation is just bizarre.