Could you add a some special inserter (or any other structure) to automate it - load/unload of near cars?
it will be fine to use it with AAI Vehicles. Scenario:
1) deploy some with the AAI Vehicle deployer (with preset of unit Data)
2) insert some fuel and ammo, and other items
3) (Optional) Give command go near to the SPECIAL INSERTER
4) the inserter load it on the train
5) the train goes somewhere
6) unload them, and start acting via Unit Controller somewhere there far far away.
7) PROFIT!