Alright, I solved it with a workaround. Thanks a lot everyone!
Apparently, as @iseries pointed out, Copter either uses the gimbal or the yaw to point at an ROI. This poses a problem when using a 3 axis gimbal with less than 360 degree field of view. In my example, the camera could not point at the ROI when the copter faced away from the target.
So I disabled yaw control on the gimbal, pretending to use a 2 axis one. Thus, the copter now yaws toward the target and it is in view.
Maybe this could be fixed in the next release.
It took some time to set it up, but the Tarot 3D works fine with Pixhawk passthrough. Here are my parameters: Params13112017.param (13.4 KB)
And this is what the gimbal page looks like (I manually put in the settings I disabled due to my problem):