The red of a stop light makes a lot more sense in relation to the red of a fire mode on a gun when you think of red being "caution, unsafe" instead of just "stop". Just like the red of a STOP sign is to caution you into paying attention of the danger of the cross traffic, not necessarily just stopping.

Red lights on top of towers isn't trying to tell planes and helicopters to stop, its telling planes to exercise caution around the tower.