When viewing your recipe you can click on the name of your beer and change the type of process (extract, all grain, partial). This will adjust the contribution from crystal malts a bit. If you try changing an extract batch with crystal from 'extract' to 'all grain' then you'll see the gravity increase even more because you'll actually get more fermentables (or better efficiency) with mashing.
Steeping grains are generally already converted grains and you're just extracting their "goodness" (i.e. flavors, aromas, and sugars). Since the sugars are already converted and will be extracted when steeping then they will add to your overall gravity which is why they raise the gravity in your brew. Therefore, what BrewR is doing is technically the correct way of doing things; now, how much those steeping grains will contribute to the gravity may not be accurate but it should be close.