Good observation. In Peopleware: Productive Projects and Teams the authors specifically address this phenomenon. Programmer productivity varies widely between organizations and a lot of it comes down to environment.
I got the impression that the paper was suggesting an early, disposable prototype during the preliminary program design phase, similar to what Fred Brooks suggested back in the day. (http://c2.com/cgi/wiki?PlanToThrowOneAway) Meaning that the PPD phase was in effect an initial iteration through the development process. The outputs from that were used to generate the program design documents in the primary development process.