I don't mean to say they're separate. They just don't operate on exactly the same track.
For example, let's take the French system. If you go from Lyon to Paris, there are a number of stops along the way. At those stops, if you looked at a map, you would see all sorts of feeder rail lines going into that particular stop. They would be operating on low-speed local regional service and they connect into the TGV and away you go.