I'm not sure auto detect is the best idea. Since the load/unload objects are wider than the track, anyone using it would need to know that ahead of time. Then you also have issues of prexisting worlds adding this mod and what that would mean for the auto detection (kind of the same issue as the first really).
I would almost think having the load/unload as placeable items would be better (keep it simple). You could keep the GUI and have it essentially place down blueprints of the load/unload that will mark anything in the way for destruction.
Additionally, keep in mind that you may want to have a loader over an engine to fill with fuel, so just skipping those spots might not be the best for everyone. With the ghost/blueprint idea, you could just cancel the ghosts you don't want, and undo the destruction of stuff you already have.
The other option would be a bit more difficult on your side, where you have the GUI in its own category tab (like the existing "Trains on the way" and "Trains with this stop"), and then you can have more information about the stops. Maybe a bit like setting up stops for a train where you add a stop/station (spot where car sits), then specify if it's load/unload/spacer (spacer is just plain track). You might even be able to specify whether it's cargo or fluid (if they show as ghosts, the different types could take pumps over inserters in their recipes). Like I said, a lot more work.