The only way they could make something like that work, is if they either did away with eyes of the universe (so you don't know where every ship in the universe is on the minimap), or massively scaled it down (which they should do anyways).. to make it difficult to keep tabs on the vast area of space your empire occupies... and if you did attempt to keep tabs on all your areas, it would be something that would cost economically.
That way, only ships that are actually 'spotted' could be told to leave. If you don't know they are there, you can't tell them to do anything. Ships could be flying through your territory and wouldn't know it, so you would be unable to do anything about it.
But to have civ's unable to enter your territory due to your area of influence really doesn't make much sense, since it's not exactly 'territory', as territory is on the earth (actually landmasses and borders filled with populations of individuals).