In GT1 it's because both the XRR and FZR would need to be slowed down to match the pace of the FXR, though over a season the FXR does sometimes have its advantages (easy to control, less fuel, better at slower tracks). Although MoE is just 1 round this season, the time taken to properly balance all 3 in GT1 for the amount of teams who would drive it is just not worth it.
In GT2 all 3 cars should be balanced, because it is easier to balance cars when you have to add restriction to all of them to start with.
However in general, AWD cars are not used in real life GT racing therefore it would be wrong to have the easiest to drive car on the same speed as others, because everyone would choose it.