I agree that the software is looking at it very black and white. The problem is, it's colorblind: It doesn't know it's missing this feature, thus it's not computed. S3D only deals with overhang, it appears to have no concept if an item is touching the build platform or not.
Let's compare against other slicers:
Makerware, Cura, and Slic3r can all do this, easily. No crazy tweaking is needed. No compensating for overhang angles, because this isn't an overhang issue. This is an 'unsupported floating feature' issue.
This either falls into a bug category, or missing feature category. I really don't care which, but I'd sure like it to be "supported" (get it?