When the ingredient Type is set to Honey, you can enter the brix value without converting it to the "one pound dissolved to make 1 gallon" value that's used for grain.
The measurement difference is probably due to the fact that BeerSmith uses the sucrose value of Brix refraction. The document you cited seems to be adjusting for fructose.
Various sugars have slightly different refractive values. The difference is minor enough that brewers are ok citing the refraction of maltose and dextrines in in the sucrose scale value. There are adjustment calculations available for better precision, if desired.