You wouldn't need two completely independent systems, you could have the stations separated with a partition that keeps the pre- and post-security portions separate. The Skytrain at MIA operates very similarly. Half of the system is to allow for passengers inside security to move from one end of the large terminal to the other end. The other part of the system picks up incoming international travelers and takes them directly to customs. All passengers are riding the same train, but are forced into their respective cars based on if they are in the international or gate section of the station.
While it's neat to read about how the airport's construction was designed with the AirTrain in mind 30 years before it became reality, it's a shame to know that its overall failure was due to cutting corners (or not, since they decided to not accommodate larger trains?
) and taking the cheap route. Hopefully the replacement would be an AirTrain 2.0 that is better designed and future-proofed for growth. From my experience, airports with non-road methods of transportation are much easier to navigate than airports where a bus is needed to reach the terminals. Even the AirTrain at EWR, despite its many problems, makes it very easy to get around if you're traveling off-peak in good weather when the train is functioning.
When the eventual replacement time comes, it will be interesting to see how it affects the rail station. If airport transportation were to revert to buses (*shudders*), I guess some new kind of connection would be put in. If AirTrain 2.0 becomes reality, unfortunately they would likely need to shut down the station again like while the AirTrain was closed a year or two ago.