If I understand your question correctly, it is not the "engines" that load into Driver Setup, but drivers.
There is a check box at the bottom of the Driver List, "Generate new Drivers for empty trains", that, when checked, will automatically assign drivers for every empty loco (or driveable vehicles) that do not already have an assigned driver in your Route/Session. Unchecking this will prevent drivers being assigned to "empty" locos.
Another check box, "Remove all existing Drivers first", will remove all assigned drivers from their locos. If the two boxes are checked then you will get a new random list of drivers assigned to all locos every time the Session is loaded.
