A module can be functional, in that it behaves as a module even if not implemented as one (and certainly need not an isomorphism between genes and anatomical or behavioural features).
Chomsky argues for theories that make sense; whereas Norvig accepts impenetrable machine learning model as theories. http://www.tor.com/blogs/2011/06/norvig-vs-chomsky-and-the-f...
Unfortunately, biology is messy. But I think we should at least try to decompose it into what it is trying to do.