Ideally, any energy loss that is caused by a mismatch of torque conversion should able to be corrected by employing the correct diff ratio. And hopefully that should fix any energy loss. I like to think the slightly bigger box ideally shouldn't cause any significant loss of energy, 'cos after all the interior components are near identical, but just slightly bigger. A heavy duty clutch may be necessary to match a high revving RB30 with the TB42 gearbox.
There is a thread somewhere on how to fit an auto tranny onto a GQ RB30.