You're good.....but....
I too am a die-hard GTD'r who uses Pomodoro (about 6 months now) to keep me focused when i'm actually in one spot for long enough to. I use a timer called "It's Focus Time" app, because it (as opposed to many of the other sim. apps) has a clicking timer sound if i want it. I read somewhere that this helps and it seems to.
The question i have always had about using Pom, is the effect that it could have on the state of "flow". Flow is the state where you are fully engaged in what you are doing, and time doesnt matter, and you love it. Like when you are writting something or painting or whatever, and after several hours you go, "wow! it's 2:30am...what just happened?" The goal is to increase the time in flow. If I feel like i am "in flow" then my Pomodoro timer going off is a bit of a "flow buster". I usually just reset it and keep going without the 5 min. break. I know that Mihaly Csikszentmihalyi, the psycologist that came up with the concept of flow, is a major GTD's himself as is his staff, but never heard what he thought of Pomodoro as it relates to flow. Interested in other's perspectives on this.