You certainly don't need SH3 commander for the game to load the right colours (Atlantic/Arctic/Med) according to your location. As for whether or not they change in realtime as you sail around, I'm not sure. Anyone fancy sailing through the Gibraltar straight to find out?
One thing I do know is that environment colours (including sky and reflection maps) 'morph' from one set to the next according to time of day... so I don't see why they wouldn't change in realtime according to location as well.