I think the main problem with the countdown is that it's based on your computers framerate. This means it will be slower the less FPS you have, and faster the more. I think that the creator adapted the countdown to 60 FPS, so on less powerful machines it will count slower. It would also be better if it counted faster, though :)
I may add a 30fps mode for slower machines. But yes, the game runs per-frame right now so that high scores are independent of your graphics performance.
If you have your timer like so
float time = 0;
time = time + tineSinceLastFrame;
Adapted for your language, then it would be accurate on all machines. I think this is especially important with highscores. To find the time since last frame, you might be able to record the system time in a variable, and then find the change. I'm not sure if this is possible using your engine and language, but it would be a great improvement. :)