Not in the least. I have a GYT-R off-road flywheel on my '06, and if anything, it pulls harder at low speed with it than without it. I'll guaranty there's no loss of performance.
Why a flywheel weight? Defeatng the purpose of installing the 06 cdi.
As was pointed out, the quad engine is a low power version of the WR. It's down about 8hp to the YZ, and comes with a flywheel 3 times the size of the YZ's flywheel. The YZ450 flywheel is smaller than the gas cap, and weighs next to nothing.