it applies to any "on click" effects so anything that automatically clicks for you gets buffed by that tree as well

Does that means it only applies to manual clicks and auto-clicks weapon damage augments? Or does it also includes the maximum damage phase? I think it doesn't because when I upgrade this tree I don't really feel any improvement.

it does include maximum damage phase, the clicks can potentially deal more damage than the team but they have to be aimed which often times just has them shoot at then air, it's definitely not noticeable when you're overpowered but if you're trying to reach a higher level it can make a huge difference due to how powerful click damage is