Yea, the default on both games is one tick below halfway. In the scripting, all timings are in a time unit that's defined as "1/10th of a minute", and this is only true on that default game speed.
As for the countdowns... they're part of the scripted missions, and in many scenarios, they're not just mission fail timers, but something actually happens after the countdown ends. I don't see any point in changing that.
But I guess you can edit the scripts with a map editor like RAED or Mobius Map Editor and just remove that part?