I'm assuming that the application first compares building heights to the nominal 400-foot AGL altitude limit: 400-164 equals 236 feet of vertical airspace in which it's legal to fly even before you consider the structure exemption that would permit 564 foot AGL within a 400-foot radius of the building. Calling it a math error was a bit of a misnomer on my part.

I'm still not quite sure what calculation would have a marked location like that as a "no-go," and re-reading the error messages doesn't really clarify the logic. When it says "too tall to clear safely from there" I'm reading that as the building is too tall and thus you can't fly above it, but that's clearly wrong on two levels. Likewise, the building height + 400 feet was still well below the floors of the relevant Class B and Class C airspace shelves around SFO and OAK. Best guess is that the 80 foot exclusion zone around a building the program applies is probably to blame.

There are some other problems I noticed, but I'll send those to the OP via the feedback form on the site.