Any labor needs to be billed to someone - the dealer's not going to willingly put their techs on upgrades for free, so they have to charge Smart corporate. It's possible that part of that $1,020 is labor and whatever else was needed to get that 2.0 upgrade. Maybe it was billed out at an insane "corporate" rate that only looks good on the books, i.e. for tax deductions.
Think of a doctor's visit - you don't think they really get by on $20-50 per visit... they bill the insurance $250, and the insurance says "paid $80 per contractual agreement."
Don't fret over the internal numbers dealers and corporations throw around; what affects you is the end price.