> this does not sound to me like we know the "function" of these genes, only that they're nessary for each phenotype

But they're not even measuring the phenotype. They're using the transciptional signature as a substitute for phenotype/cell function (i.e. the bag of RNA model). This is a poor substitute if you try to apply this to practical applications such as cell engineering. Let's say I perturb a cell to match it's transcriptional signature to that of a neuron. Does that make it a neuron? Not if it doesn't function like a neuron.