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!

Copied the idea to the original old mod discussion too: https://mods.factorio.com/mod/Vehicle%20Wagon/discussion/5df153461c14d8000b2dbebf

I've picked up script development for Vehicle Wagon, and I'm open to adding a mod interface so that other mods can command load and unload operations. The hardest part will be making it work with AAI Programmable Vehicles, both because it will require using a mod interface to communicate with AAI, and because I have no idea how AAI even works at the moment :D PM me on the forum and we can talk. If Earendel is interested in helping, we might be able to get it to work.

I love the idea of automating the vehicle wagon 2 insert and deploy automated vehicles with a dedicated structure. Despite the probably huge amount of work required to make it work with AAI Vehicles, any progress so far?

I did some experiments with a "loading ramp" that you could drive onto manually to load the vehicle without the winch or getting out. Didn't get very far. Experiments with adding a "ferry" to Cargo Ships actually had more success, though not enough to release.

Having looked into a bit, I don't have much hope for autonomous intermodal trips. You would need a way to define two entirely separate AI programs for each end of the trip, and a mod to remember and restore those AI programs when the correct vehicle is unloaded in each spot. I've stepped away from modding for a bit and it's more than I want to take on.