Depending upon the model for bitterness that you use, the program may or may not compensate for the higher gravity of the wort. The Tinseth model does take the average wort gravity into consideration and this is the default setting for BeerSmith. Rager does not. I cannot remember if Garetz does or does not include the gravity in the model.
Be mindful also that the bitterness models are only an estimate for the amount of isomerized alpha acids and not a direct measurement of the perception of bitterness. Depending upon your hopping schedule any IBU model can be more or less accurate to the original intention of the recipe. The actual accuracy of the models is also highly dependent upon your process, so take any number with a large grain of salt.