Hop utilization

Does the BeerSmith2 take into account the approximately 20% loss of IBUs alpha acids in the boil and fermentation?

"...Stan Hieronymus goes further, discussing work by Tom Nielsen at Sierra Nevada that indicates an IBU loss of approximately 20 percent during fermentation."

Only to the extent that any of the formulas available portray that, which is to say, "mostly no."

And if it's that critical, you need to adjust every recipe you come across because nearly all are using Tinseth or Rager, which are post-boil numbers.

Post boil calculating is somewhere between voodoo and fortune telling. If you're aiming your numbers at post ferment or at bottling, then you'll want to just get an array of your beers tested in a lab. Your equipment and process are huge variables. That SN number is accurate for them, but anecdotal for the rest of us. There are other papers that state as much as 50% loss in Pilsner brewing. Plus, SNPA, Torpedo and the rest were created by flavor not from lab measurements. Those came later.

Running with a set of untested assumptions is like running with scissors and a kitchen knife; it's perfectly safe, ...until that one time....