There's a distinction between a full tear-down, and a comprehensive, incremental, rebuild. This is Spolsky's distinction, as I understand it. The parts of the structure you aren't rebuilding provide context for those you are. The "rebuild from scratch" scenario loses this structure. You see a similar move in architecture -- I recall several buildings at UC Davis which were largely rebuilt from the inside out. Expensive, but classic facades were retained as an overall win.
Frankly, there are cases I'd go one way or the other. I do think that the "learn from your mistakes" message is a valuable one, and is the core of his argument.