Hops must be the most misunderstood part of brewing, personally I think all the calculators are Voodoo and at best give pretty rough approximations, the big brewers mostly use a large amount of experience backed up by good lab reports to get accurate IBU results.
If you have made the same beer in the same brewery using the same hops (POR for example, alpha only moves around % or so from year to year) a couple of thousand times, then measure the **** out of every batch; you are going to be able to say with a great deal of confidence what your utilisation is going to be.
We as home brewers rarely make the same beer twice running; we use a vast range of hops, wildly varying wort gravities and hop additions ranging anywhere from miserly to ridiculously, no big surprise that we rarely know precisely what we are ending up with.
I have posted this before but its well worth reading
The HBD Palexperiment Results
When 40 brewers brew are asked to brew the same beer with the same hops the range IBUs looked like this
The results for the best calculator were a bit of a surprise to. None of the well known calculators could be regarded as giving the Right answer, big ups Randy.
Just to make it more interesting, IBUs are measured in finished beer, even if you could calculate the exact end of boil bitterness, both Alpha and Isoalpha acids stick to everything, fermenters, flocking agents, trub and yeast included, the bigger your yeast pitch the more isoalpha you will pull out of your beer (no Im not suggesting you under pitch) to the point there can be a 30% variation in the IBU of the same wort brewed under different conditions.
Like I said its all Voodoo, do your calculations, brew your beer and just ask yourself if your beer is bittered the way you want it and adjust accordingly next time.
Mark