The second law doesn't say that things converge towards a spatially uniform configuration. The second law says that the physical systems evolve towards states of a greater entropy (a measure of disorder). It's a completely different thing than uniformity. What Robert presents as "our intuitive understanding of the second law" is actually completely orthogonal to the second law. It has nothing to do with it in general. ...
Yes, gravity tends to clump things. They evolve into "compact" configurations. But this fact is in no tension with the second law of thermodynamics whatsoever. The only reason why Robert thinks that there is a tension is that his thinking is sloppy - perhaps deliberately sloppy. The existence of the attractive gravitational force is not only consistent with the increasing entropy: one makes another more natural in this context. In fact, the maximally clumped configurations of matter tend to maximize the entropy - they're the black holes that carry the maximum entropy that can be squeezed into the same volume.
Whenever attractive gravity dominates, higher entropy becomes associated with non-uniform matter distributions, and these two descriptions therefore apply to a typical state of matter in the future. The previous sentence may sound counter-intuitive to someone but if it is so, it proves that his or her intuition is failing completely (because every sensible person knows that gravity naturally clumps things and future configurations naturally have a higher entropy so clumped objects that will actually be created or evolved in the future must have a higher entropy). The emotions show nothing wrong about cosmology, thermodynamics, or their union. Science is not about the emotions or intuition of uneducated, slow people with bad scientific intuition.
Although it may sound unpopular, there are many fewer people than 6 billion in the world who can actually use their intuition to answer both deep and elementary physics questions, and Robert is unfortunately not in the lucky group. Well, I know that people prefer to hear that everyone should build on their intuition because everyone, including mediocre crackpots of Garrett Lisi's caliber, are new Einsteins. Well, people like to hear it but it is a lie. There are only 100-200 intuitive Einstein equivalents in the world and none of them thinks that Lee Smolin or Garrett Lisi is a good physicist. Everyone else - about 6.5 billion people - should mechanically learn the important insights found by the smarter people.