I'll try explaining it more clearly.
I'm playing with SS+, Nexerelin and several faction mods. Combat and Technology skills are maxed.
1) I press the left mouse button and hold it down to fire all three shots. I keep pressing it down. The cooldown meter starts decreasing from right to left, goes to zero, then begins another, shorter cooldown from right to left. Only when that second cooldown is over does the weapon start the firing sequence again. Left mouse button is continually held down throughout all this.
2) I press the left mouse button and hold it down to fire all three shots. Then I release the button. The cooldown meter starts decreasing from right to left, goes to zero. There's no second cooldown, the firing sequence starts as soon as I press the left mouse button again.