When you use Vehicle Wagon 2 to put a vehicle on a train, any packed boxes on the vehicle are empty once you take the vehicle off the train. I don't know that this is a huge deal. I mean, you could just pack the vehicle and put it on a cargo wagon and not use Vehicle Wagon 2. I just thought I'd mention it.

The other mod stores inventory contents as simple item stacks, basically just a name and quantity. While it works great for most items (an iron plate is the same as any other), some items have more data than that and when the tank is rebuilt it puts a generic version of it back in (I would also recommend not to put power armor in a vehicle wagon). Unfortunately there really isn't anything I can do about this. It even has a new unique ID so I can't identify which chest it was supposed to be. It would have to be fixed on their end and would likely be an involved change.

In the mean time, you can pack the vehicle into a cargo wagon and it will keep the inventory.

I figured something like that was going on. IMHO, Vehicle Wagon 2 should just have the vehicle wagon itself have the inventory. Individual wagon types are created for each vehicle, and it transforms the base platform wagon into the appropriate wagon type when loading the vehicle. So, that would be the ideal time to just transfer the inventory from the vehicle to the wagon, and the reverse could be done when the vehicle is unloaded.

But, that would involve a major change to how that mod worked. And discussing how some other mod could change in the discussion forum for your mod seems silly and pointless. :-)