I have also been thinking of this. I think that Beersmith calculates its specific gravities based on cold liquid.
If so you would have to, as you examples suggest, add water to the boil volume to compensate for the higher SG, hense the shrinkage.
Having said that, the difference is so little, that it makes no sense for me to adjust. I'm not saying that Beersmith shouldn't take it into account, but only as comfort it doesn't change much for me. As a homebrewer my equipment is so imprecise anyway that Beersmith predictions will always be off. For instance, the way I read the volume of the wort in my fermentation bucket. I'm not so sure that the sticker on the outside of the bucket, indicating the volume is that accurate. And on top of that comes my reading. Lying there on the floor trying to get a leveled measure. And lastly my hydrometer readings are also not that precise. I look at it at guestimate it, probably with 1 SG error margin.