We've taken this to be that any of your pieces would count as a presence in the system. The overall description says that you use it when defending in combat. The sentence that quoted seems intended to qualify that it is in effect even if you don't have a fleet or starbase (you do not HAVE to have a fleet or starbase). If they intended to make it only effective with an outpost or colony in the system, wouldn't they have stated that an outpost or colony is required?
I believe you're right. Unfortunately, in the absence of any other definition of presence in the rulebook, one might be tempted to think it means "i.e. a Colony or Outpost."