You can look at it as an agile process. You don't model your whole project at once, but when you start a Pomodoro you commit to working focused for 25 minutes. When the time is up you can prioritize differently or make a push on an unplanned item.

Also, I totally agree on your in-the-zone statement. I currently only use Pomodoro when I am having a slow day and I don't want to let the procrastination get the best of me. When I am in the zone I don't need Pomodoro to help me! =)