Exactly! You're intuition is correct. That is the 1.002 gravity difference.
The 0.4% difference is negligible for most brewers. In a very light session beer that you're describing it has a bit more meaning and influence. In the US, any beverage under 0.5% is considered non-alcoholic. That was my reference point in saying "negligible."
The other reason it's not accounted for in BeerSmith is that priming sugar is added after the brewer has made their "final gravity" measurements. In fact, I don't think there are very many recipes (if any) that consider it when stating the potential alcohol. So, it isn't just BeerSmith, it'd be any brewing software or standard brewing technique to ignore the alcohol contribution of priming sugar.
I guess it is meaningful to commercial brewers who are taxed on alcohol content. If that's your case, then it just has to be a part of your procedure to add it as a matter of course.