Torque PIDs

So I’ve started to tune my 2.8 Duramax now after completing the 2 diesel courses, I first got familiar with logging the stock tune and moved to making small adjustments then logging more etc.

So I can log some torque PIDs and after adding fuel, boost etc. these torque readings are lower than stock, what’s the deal with that?

is it just because they are calculated torque readings and tuning messed up the math?