How about this scenario. (Elaborating on what Checkboard and Old Smokey have said)
You have an MEL that requires a 10,000kg reduction to takeoff limit weight.
In this situation, they are effectively saying (depending on which MEL it is, and why the performance penalty exists) that the aircraft will perform, on takeoff, as if it is 10t heavier.
You have calculated that for the given runway, its 30 degrees outside and you can take off at 150 tonne using FULL RATING. The MEL means that you can now only take off at 140tonne. If you are at 140t you really going to derate your thrust to the 140tonne figure? After all, the MEL has said you are performance limited to 140t! Full Rating Please.
If you are 135t - You are reducing thrust as if you are 15tonne below the performance limit weight, when you are actually only 5 tonne below. If you added the 10t to your actual weight (135 + 10 = 145), then you would get the appropriate conservative derate. Note, that you are working your performance out on 145t, but only taking off at 135, which is below your adjusted limit weight.
Clear as mud?
When I try to understand it, I just think that the performance pentaly MAY mean that the aircraft performs as if it is that amount heavier, and think about taking the conservative option.