You missed "clear property boundaries" as a difference. It's very easy to tell if a chemical compound is being used by two different firms, it's the equivalent of the source code being identical. But for software patents, there's much more subjectivity involved, e.g. does your patent cover this type of swiping, even if it doesn't in reality could you possibly convince a jury of ordinary people of that fact?.

This ambiguity is bad in itself. You might not like the chemical patent, but at least you'll know for certain whether you infringe it or not, which saves a lot of court battles.