BeerSmith does not modify the color for length of the boil - as far as I know no one's software does. The Maillard reaction that darkens the wort is not well modeled and includes a lot of variables beyond boil time, so I don't have a good equation to simulate it in the program. Further complicating this is the fact that the reaction is much more pronounced for extract than all grain brews. In fact most all grains see little in the way of extra darkening. For extracts, we also have the significant problem of storage - how the extract was stored and for how long often creates significantly more darkening than you would get just from boiling it. So its not as simple as "boiling for X minutes darkens the wort by Y".
BeerSmith 2.2 does have support for unfermentable carbs now - they are correctly handled when calculating FG. It is a new feature in 2.2.