Thanks for your question. AAI creates "dummy characters" to ride in vehicles so that they will drive. Pi-C gave me some code to detect and destroy dummy characters when loading vehicles. I will look at incorporating that when I get a chance. However, there is an additional step that will require work on the AAI side for it to be seamless. I know AAI can transfer the settings when a vehicle is replaced with a different entities, but I don't think it can save the data indefinitely while the vehicle is loaded in the wagon. You would have to start over with the AI when you unload it. Unless I do something like create a new surface where loaded vehicles are teleported, so that they still technically exist...
The next feature I'm planning to add is a loading ramp that can be automated. It'll be a little while because I'm working on a different project right now.