The course you know as Pacific Dunes is my fourth routing for that site. The changes were all developed as we got to know the site better, and with some input from Mike Keiser and his friends. But all the changes were made for POSITIVE reasons, and so the fourth routing is far superior to the original.
(And yes, you'll see the process if I ever find time to finish my book.)
More often, however, one makes refinements to the routing because of outside influences -- environmental, developmental, etc. -- and in those cases the final routing may or may not be a better golf course than the first version. On the other hand, the first version could never have been built.