In TWOK the ship was operating under basically normal situation. In TSFS, where the honeycombs changed color, the ship was operating under different situations. First, the ship was following a lot of battle damage, and getting ready for a couple of weeks of repair. Then it was operating under the automated systems. Neither of these were normal functioning. I just figured the different colors in some way represented the different operating situations. The colors were a visual for the crew to recognize a different "power" situation on the ship or something.
It may not make sense, but it works for me.