All of the common algorithms for forecasting IBUs take the gravity of the wort into account. The higher the gravity, the less the IBUs.
There is some debate about whether or not this is true, and whether the reduction in IBUs is caused by just gravity, or the amount of break material, or possibly some other factors.
Beersmith does not report the actual IBUs. It reports the estimated IBU's according to the algorithm being used.
If you design a recipe, and using that recipe, switch the bitterness formula between Garetz, Rager, and Tinseth, you will probably get 3 different IBU values reported. Obviously, the actual IBUs achieved will not depend on some setting in Beersmith.
You could do an experiment by brewing the same beer twice, once using late extract additions, and once adding all the extract early, and seeing if you can detect any change in bitterness..