The grey parts of the settlement icons are to add a little depth to the otherwise flat symbols. It's a little experiment to try and make our symbols different from what has come before. We tried them out in a number of different variants, and this is what we ended up going with.

I'm still on the fence with these —*I think that they're nice when viewed up close, but perhaps a little too detailed when looking at the map as a whole. I'm not sure that what they add is better than the clarity that comes with pure black symbols. I'd love to hear your opinions on this.