The conversion factors take a measured index of refraction and give you a SG assuming there is only water and sugar. Ethanol has a slightly different refractive index than water, so your measurement won't convert exactly post-fermentation.
(I don't have Beersmith - I use other software - but I assume it's the same.)
I don't own a refractometer but I was doing some research and I found that the alcohol in the sample alters the reading. To compensate you need to use a refractometer calculator. It seems to work like the SG to % alcohol calculators.
Now I'm wondering how temperature correction works for refractometers.