Chemotype refers to the cannabinoid/chemical profile the genes create (so high THC/low CBD vs high CBD/low THC, balanced THC/CBD, etc) where phenotype is the overall expression of the genes (aka genotype) affected by the growing environment. So for example the genotype Sour Diesel can be a shorter plant if grown in high light intensity or lanky in low light levels (different phenotypes of the same genotype) but will always be the same high THC/low CBD chemotype. Most growers are interested in the phenotype as it includes the flowering time, yeild/weight, PM/pathogen resistance, flower structure, etc and not just the chemical profile of the plant.