Modal abilities will only activate after recovery is finished, but can be deactivated at any time.  For penetrating shot this means that you can turn it on, wait for the arrow to hit, then deactivate it before recovery begins.  It can then be activated before the next shot.  With proper micro, penetrating shot has no downside whatsoever.  This probably effects other modal abilities as well, though some benefit from it more than others.

 

Modal ability deactivation should be governed by the same rules as modal ability activation and require you to be out of attack animation and recovery.

This is a non-issue because the recovery time penalty is applied "on attack launch" or something, so that when you make an attack, the recovery for that attack is slowed even if you de-activate penetrating shot after the attack.

Here's a video.  It only happens every other shot though because modal abilities don't seem to activate at the first possible opportunity.

https://www.youtube.com/watch?v=SzxWhyQfdDY

Edited March 4, 201510 yr by roguelike

It actually looks like the penalty to recovery time is not being applied at all, rather than it being an issue with activate/deactivate - I'm currently at work but I can have a look when I get home. I know that in v392 the recovery penalty to cautious attack was working properly.

Tested this out myself, you can in fact disable Penetrating Shot during the animation to avoid the recovery time penalty for a single shot.

 

My understanding is that if Penetrating Shot was active when you fired the shot, it should apply the reduction to recovery time regardless of whether you deactivated the modal or not.