The larger rooms still have the 50% debuff for move speed. They have more area for crew to be meandering in than the vanilla rooms, so they will always be more inefficient then vanilla. I think a scaling modifier to the room speed based on the size is the best way to go about fixing this, where the 3x3 and the 4x4 have (completely arbitrary and probably imbalanced) 40% and 25% debuffs respectively.