But unless I am misunderstanding what is being said
OK, don't worry, the thrust of the book is that biology has changed its thinking a lot in the last couple of decades but no-one's really bothered to explain the changes to the general public, so we're all really behind the curve now and need to get up to speed.
There's a lot to take in so let's do it in stages.
So the first point to grasp, and grasp firmly, is that the genome is no longer thought of as a blueprint, or the genes as instructions to build an organism, or proteins as sort of organic machines, or the body working like some sort of organic machine or computer programme. The problem of how genotype (the genes) becomes phenotype (the observable traits) has not really been cracked despite all the work on the human genome project since the 1960s.
The second point is our desire to map things 1 to 1: we want to see 1 allele 1 trait, different allele different trait etc. but it does not fit well with the evidence. Lots of alleles may contribute to a trait, and in very messy ways. Shank colour in chickens' legs springs to mind.
The third point is that the conventional narrative is all about coding proteins, but only 2% of the genome codes proteins. What on earth is the other 98% doing then? It can't all be junk in the evolutionary attic! This was sort of rubbed in when the human genome project discovered that the final tally of protein-coding genes is a little over 20,000; apparently most biologists don't believe that is anything like enough to make a human. Surely there must be more instructions needed to make something as complex as a person?
Then, what is passed on to the next generations is not genes, it's the whole genome. Natural selection works on the organisms that carry the genes, not on the genes directly, and it's the phenotype, not the genotype, that determines fitness. (Indeed, some argue that natural selection works on the group, not even the individual, but let's park that for the time being.)
And a genome can't build a cell. Rather, the cell is a precondition for anything the genome can do (p. 94). An organism won't spontaneously form, so "a genome sequence can never fully specify an organism: how it will grow, how it will look, how it will behave - in short, how it works." (idem) Ball reasserts the role of the cell as a key functional living unit, at least as far as I've got into his book.
A big problem is that the gene is not alive. How something not alive turns into something alive is still a mystery. The gene has been too atomised to actually explain how life works. "Genes do not produce life, but on the contrary depend on it." (p.104)
So how does this impact so far on the mutation that stopped a hen sensing that her clutch was complete so she should stop laying and start incubating, with the result that she didn't go broody and just kept laying till her body was spent? In short, it's probably not 1 mutation in 1 hen; it's lots of mutations in lots of hens, randomly caused in different places and times, some of which have the same effect, albeit by a variety of different routes, with one last little change or other that in combination with what went before was 'the straw that broke the camel's back'. Many people here have hens that never go broody and lay all season long, that are not production hens; I have some, you have some. Commerce took the 'best' of these types and honed them into birds that, with artificial light and food, lay for about a year and are then discarded as waste, because they are unfit for continued commercial production. They did not do rocket science. They just exaggerated traits that nature created.