This has come up a few times recently, and there is a valid argument that specific gravity does not impact hop utilization as directly as most of us expect. However, after lengthy debates and equations, the end result is always fairly similar: the Tinseth formula (BeerSmith's default) is still a valid means by which to approximate IBUs in small brew lengths.
So, keep using BeerSmith in the intuitive manner that it was meant to be used. Most importantly, use the same means to estimate IBUs for all of your recipes. That way, you'll have a baseline "feel" for what those numbers mean in your brewhouse, even if they aren't as accurate as lab results.