Yeah, once you're in that state of flow where time ceases to exist, that beeping snaps you right out. I think the key is to find the time chunk which gets you up to that point where you're just about to feel mentally exhausted.

For me, the Pomodoro is the starting point, so 1 Pomodoro to get you to focus for 25 mins. After that, you can a take a quick break, but for the 2nd Pomodoro, you simply disable the alert, and let the timer run on.