The 3% loss is what I first said. It's the loss of ram air affect. This means that now you air bypassing air and the engine is basically sucking air in. With the bypass in the closed position the air is being rammed into the inlet. This is where the gain is.
I'll make this clearer. Tq limiter is set via oil px from the Tq ring in side the prg. The Tq oil px equals at over Tq at around the 104%ish mark. Tq limiter wf loss before this is a problem with the limiter and not the engine or and indication problem. You will never over Tq at 96%.