I can't find an official reply from Cuaron but we can rule out a preference for the film look, as this was shot digital anyway.
Maybe the robot rig couldn't hold a beamsplitter? Maybe budget/time constraints? Or he just wanted fewer constraints and less on-set chaos.
A ton of directors of postconversions have claimed they shot for 3D, but I have yet to see one that feels like that was true.
Cuaron is the first director aside from Cameron who I'm trusting to do it right. This Iris rig makes me all the more hopeful.
As for the film itself, it has the potential to be very polarizing. It's been compared to Tree of Life (which flew over my head) in cinematographic ambition, but also its divisiveness.