I always thought it was just to let you know which planets would get the stat boosts in case you wanted to convert them to core worlds. It may be that once upon a time Colonies did get the boost and they didn't change the starbase display when they changed the mechanic.
BTW - I tested one of my systems with an empty planet in the ZOC of 3 starbases and its base stats did not change when I colonized it.
