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BeerSmith will account for late extracts in the bitterness calculations. I do not account for subtle color change - the carmelization effect of a full boil vs late extract boil is difficult to calculate precisely as far as I know.
I have (personally) found BeerSmith to be fairly accurate as to the PERCIEVED IBUs, inasmuch as I have been experimenting with ONLY late additions (ie; 20 min, 7 min, flameout & dry hoppping) with some excellent results. As substantiation, a fellow brewer tonight asked how I achieved such a great "hop bomb" in the mouth without the over the top bitterness normally associated with larger (12oz/5gal) hop additions, and the response to my late kettle additions was met with "what made you try that?". BTW that brewer went so fa as to state he preferred mine over Russian River's Pliny the Elder (a very hoppy IIPA) ....... to my surprise.
And I think BeerSmith did a Great job as far as color/caramelization, albeit with my "siimple" recipe. Kuddos Brad, whether this was your aim or not.