Here's a good comparison of some of the larger boxes available.
Thule Motion XT XL Review | OutdoorGearLab
We had a Thule Atlantis 1600xt, and now a Thule Motion XT XL mounted to our 2015 4runner limited, on factory cross bars.
Two negatives I experienced with both of these carriers on the OEM cross bars:
1. With the low cross bars, and max forward placement of the cross bars you are limited in being able to move the carrier forward/rear. You are limited in how far forward you can move the carrier, which you may need to do so it doesn't hit the rear hatch.
However, if you move it to far forward, the front of the carrier overhangs the front bar, resulting in turbulent air flow and bouncing of the carrier box against the roof. No bueno. Move it too far back to stabilize at higher speeds and it'll be hitting the spoiler when you open the hatch.
2. With how low the cross bars are, even if you get a Motion XT which has an antenna notch at the rear, the carrier rests on the antenna, and creates a visible distortion in the roof. No bueno. Even moved forward to the maximum resulted in this for me, same with the Thule Atlantis. I overcame this by replacing the antenna. For you, this is probably not an option since the sharkfin shape and contents changed in 2016? I believe.
If i were to do it again, or didn't have OEM cross bars, I would get a set of 2 Thule 7503 aeroblade edge bars, which sit slightly higher than OEM, but still look OEM-ish, and can be locked.
See
this link at etrailer for details. They also have a few pictures and at least one video with these bars on a 4runner.