Searched Raybestos Brakes' online lookup, entered 2012 for the 5th-gen and 2006 for the 4th-gen:

Rear brake calipers
4th-gen has a larger piston, 2"/50.8mm vs 5th-gen's 1.89"/48mm.
All this time I assumed GX470's use the same rear calipers since they're the same 120 chassis as our 4th-gens. According to Raybestos the 5th-gen caliper is also used on both GX470 and GX460, 1st-gen Sequoia, and 80-series Landcruiser/LX450. I wonder if the GX470 is a misprint I'll try remembering to write down the casting #s when I rotate the tires on my folks' GX.

Rear brake rotors
Outside/overall diameter 12.286"/312mm both generations
Bore diameter - looked this up on Autozone, Raybestos didn't have the specs listed - 106mm 4th gen, 108mm 4th gen
4th-gen rotor also used on GX470, FJ Cruiser up to 2009, 1st-gen Seq.
5th-gen rotor also used on GX460 and 2010-2014 FJ Cruiser

Rear brake pads
Same pads for both generations

The 5th-gen rotors' larger bore diameter is what @That_Titanium_4RNR mentioned about the rotors not centering properly.

TL/DR - for best fitment stick with 4th-gen rotors when updating to 5th-gen rear brakes because they have the same overall diameter and thickness. Pads are also interchangeable.