There are a few ways, you could blend the motion between waypoints. If you put the trigger between blended waypoints the output event will be triggered as the first point enters the blend to the second point, making turning signals on or off while in motion possible. Since triggering an output does not require physical time this will not result in any sudden stop errors.
You could also place the output trigger in a background thread that is monitoring some state of the robot and then triggering an output, for instance the output is turned on or off when an operator presses a button. You could watch in a thread for the input to turn on and then trigger an output.
Not sure what hat your exact requirements are so hard to give any other ideas.
Is there a way to trigger output without interrupting robot movement?