Yeah - also, if it's an animated feature, it's a relatively minor task to make a second virtual camera with a slight offset and re-render.
The Ant Bully crew had about 200 people at its largest, and about ten were Imax artists whose job was to take the final rendered footage, create the second camera, render it out, and troubleshoot all the problems that weren't visible in 2D. They ranged from things like the camera focus sliding in and out to show great depth (not necessary in 3D), shaders for translucent objects like gemstones which had to be adjusted for refraction, and awkward placement of foreground objects which covered the action in one eye but not the other. So - not trivial, but not show-stopping either.