I want the Automated carts that spawn from your basic automated setup Train Stations to have a second "passenger car" such as WagonB. 
How can I update these carts when they spawn while maintaining the conductor limit? 

If I update the default Train Station trigger it becomes a "created train" that ignores the conductor limit, and then every single train station gets an automated cart. 

The two ways we could go about this would be to:
1. Disable vanilla spawns and create new spawns with the plugin. It seems like this bypass conductor limits though.
2. Make the triggers add wagons to new trains when taking over control of them. This would have to take into account what happens if there is insufficient space, probably need to delay spawning the wagons.

Merged post

I pushed a change to the GitHub repo which you can try.

https://github.com/WheteThunger/AutomatedWorkcarts

New config option:

• DisableDefaultTunnelWorkcartSpawnPoints (true or false) -- While true, vanilla workcart spawn points at train station maintenance tunnels will be disabled, and any existing workcarts spawned by those spawn points will be destroyed when the plugin loads. This enables you to create custom spawn points in the same location, allowing you to use alternative train engines plus optional wagons.