He doesn't say "arbitrary from a scientific perspective", he says "arbitrary". The former would be a silly point anyways. Would it make sense to point out how arbitrary it is that the houses of congress are divided up by party because party appears arbitrary from a (genetic) scientific viewpoint?

Don't confuse genetic/geographic science with science as a whole. Anywhere you can do experiments you can do science, and politics is no exception (although everything is much noisier). Certainly, the groups of people described by the census are meaningful in a scientifically confirm-able way: they identify with each other, forming clearly discernible self-selecting cliques, neighborhoods, etc.