So a couple of observations....I found that the PQ has got worse as the season progressed. It may just be my sight though. Haha. Furthermore, whilst watching the multi part "Resistance is Futile" featurette I've noticed that the PQ of the selected clips shown appears to be a considerably better than that shown in the final individual episodes. Bizarre. The episodes look....cleaner somehow.
I've noticed that the clips in all the features usually have a lower bit-rate that doesn't preserve the film gain as well. I suspect this is what you mean by things having a cleaner look, it may look cleaner but it's actually less detailed.