From my playing with the various factors presented by BF's Recipe Editor (Fermentables, Pitch Rate, Ferm Temp, Yeast Type), the only factor that seems to affect BF's calculation of FG is Yeast Type, for which BF selects the average attentuation for the yeast type selected.
The use of different Fermentables (i.e., grain bill) don't seem to affect the BF's calculation of FG; for example, listing a crystal malt instead of a pale malt does not affect FG as long as the two grains' PPG contributions to OG are the same -- in other words, BF for FG calculation purposes seems to treat all types of grains the same and doesn't seem to differentiate among them in terms of their fermentability (i.e., BF apparently assumes all are grains are equally fermentable).
In his book "How To Brew" (page 86), John Palmer states: "There are three principal factors that determine fermentation activity and results: yeast, wort nutrients, and temperature." He also states (page 63): "Attentuation is not entirely up to the yeast. The fermentability of the wort, as determined by the brewer, sets the limits to which a particular yeast may work."
In my most recent post (as of now, yet to be posted), I suggested the possibility of BF employing mash temperature as a factor affecting BF's calculation of FG, which, as Mr. Palmer points out in his HTB book (page 149-150), does have a quantifiable affect on FG.