In the same video at 3:13, you can see that the person in the front is the only one holding the stick, and just moments later the helicopter turns.

What I'm saying is both pilots can control the helicopter.

Edit:
"According to this picture, we decided to change that. http://zarco-macross.wdfiles.com/local--files/wiki:boeing-sikorsky-rah-66-comanche/boeingrah66eb.jpg [^] (Community, thanks for it)

As pilot you can fire, just set manual fire on, as gunner you can take controls, too...
As a pilot you have to have great view... In AH99 you cannot have the seats like in AH64, MI24, becose in that examples is gunner seat higher then the pilot's." -Redstone, BI Developer

Note that in the picture, the pilot seat (11) is in the front.

Nothing is shown at 3:13. Attached is a picture of 3:13.

Like I said earlier "But both seats should be able to do everything (If it is like the Commanche)" However in Arma 3 this is not the case. The rear seat piloting can not use flares and the front seat gunning can not target lock.

I can understand how someone who is not used to flying helicopters wouldn't immediately understand these concepts. Most vehicles of both land and air put the driver/pilot in the front for the best view. Having the best view means being able to see better, and obviously seeing better helps you drive/pilot better. But attack helicopters have to take into account more than just driving/piloting.

Attack helicopters are designed so that the gunner leads the pilot.
The gunner constantly scans for targets, both with optics and the naked eye while the pilot focuses entirely on the helicopter position. The gunner spots the target and then informs the pilot to move accordingly. This is why the gunner should have the best view and the pilot should be snug with the center axis for best handling of the cyclic. The seats help them do their jobs easier.

I recommend the seat defaults be reverted and/or unlock both seats to give 100percent functionality for both piloting and gunning (Flares, locks, etc.)

3:13 must have been the wrong time then, my apologies. Anyway, shortly after 3:13, if you play the video at 0.25 speed, you can clearly see that the front pilot is holding the stick.

That said, unlocking full functionality for both seats is an idea I would gladly support