That's if you believe that the mind is separate from the brain. I used to think so, but I'm seriously questioning that. We can already crudely manipulate the mind via manipulating the brain simply by what we see or hear (propaganda/etc) or smell. If we truly had mastery over the brain, doesn't seem farfetched to think total control over the mind would be possible.
As for genes and phenotype, why wouldn't controlling our genes control our phenotypes. We already control our children's phenotype to a limited degree by choosing whom to marry and have kids with. We can control phenotypes of dogs by breeding. We can create flourescent animals and plants via genetic manipulation.
Right now, our understanding of the brain and genes are so limited that we could call it the dark ages of brain and genes. But what about in 100 years? What will our understanding of the brain and genes be? If the advances are substantial than significant control over our minds and phenotypes shouldn't be a problem.