I guess they are not the same color simply because, they are assimilated, not the "home town" of the empire. In others words, they have not the same value as the north america.
Japan is in red because it's the current target.
Another thing : if you look carefully at this pic in the episode before the zoom out, you can read "Britania" . Why would they write that name if it was not a part of the empire ?
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Another possibilities is that those points were navy task fleets, movable bases, for the forces to attack from, as was seen in the Gulf War.
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If it was just some navy force, they could have been attacked by the chinese federation nearby. That would cause some trouble when they don't need it. And as Cecilia say in a episode, they don't want a battle with the chinese now.