No, it was not how the system was designed. The Pomodoro Technique should train you to have your own sense/feel of time. So, given enough time with it, you should be able to know when your 25 minutes are up, and pace yourself accordingly. It trains you to avoid the whole "I didn't realize it was already..." feeling.
It shouldn't be on top of your windows, blocking your progress! At best, it should be at the side (in the taskbar or on your table).
If you want a sense of urgency from the Pomodoro, you should make it auditory, rather than a distracting visual. That is, have an actual ticking Pomodoro timer or play the ticking sound somewhere.