The way I understand it, the amount of hops pulled from a bale to analyze for acid is minimal. THAT sample on THAT day was X % acids. Saying that the little ounce or pound bag that we buy is X% is just a generalized idea.
There are varying calculations for determining the level of IBUs in the wort post boil. I don't know which one your software uses, mine has options. Tinseth or Rager, I use Tinseth in spite that he's an Orygonian.
I would guess that my actual hops are what the package says they are, give or take 10%. My projected target IBU in the wort is probably within 10% of what the computer says, plus the 10% variance from the hops. Minus who knows how much that is lost in fermentation due to off gassing and attaching to yeast and dropping out.
I can honestly say that I have no idea how many IBUs are in my finished beers. The only way to know would be to send it to the lab.
So, saying that our beer has X amount of IBUs is technically inaccurate if it's based only on an IBU calculator. But, if you use a calculator, change the drop box AA numbers to what your package says, measure accurately, add them at precise times, chill the same way each brew, etc... you will have a good baseline to work from to make adjustments in the future.
In the end, I don't sweat the small stuff. I call it what the calculator says. Works for me.