I understand the basics that chromatography is a fairly slow and expensive process compared to direct synthesis. When a synthesis route is not feasible, the economics become favorable. Not being in the chemical industry, I do not know the specifics of these economics or how common industrial scale chromatography is.
Three applications I know of are sucrose separation from beet molasses, insulin from genetically modified E.coli, and B-Carotene from algae. There are surely many others especially in the pharmaceutical industry, but I have not been able to find a list of specific chemicals.