I created a pull request for this:
I created a command line option that allows you to give a folder that contains plugin assemblies.
These will then be loaded and all classes can then be used in your Train script.
I am also thinking about scanning the Train.exe folder and loading all assemblies in that folder as well. That way you can include assemblies on your system all the time without having to add a command line option.
The commandline option is still usable for project specific assemblies.