I enabled Automatic mode in the mod settings. When I call the train to me, I immediately go to the trains GUI to set a temporary stop of where I want to go after it picks me up. My expectation is that the train follows the "OR passenger present" wait time and goes to the next stop I just set. However, when I get inside the train, the train goes to manual mode and I have to keypress to make it go.

I have to look into that, but I think it works as designed here. The mod is programmed to stop the train right in front of you, Automatic Mode setting only does something when you don't enter the train.

Okay thanks for looking into it. What reason do you add the "OR" passenger present in the schedule? Thats what led me to this thought

The "OR passenger..." is not from the mod, it adds a Temp Stop with 1sec at your position to bring the train to you (after you pressed eg.CTRL-J ). And when it arrives it goes into temp mode to stop the train. This is how the mod is designed to work.