Chillie.....
Wake seperations start from first aircraft's wheels up to the following aircraft's wheels up. Timed to the second, i.e. no rounding up or down of minutes.
Operationally we try to achieve the closest to the required minimum by clearing the following aircraft to take-off prior to the minimum time required allowing for take-off roll required.
However, from a training perspective how can you guarantee the take-off roll time? That is probably why the instructors are getting you to issue take-off clearances after the required time has elapsed.
Hope this helps