To add a bit of context, trainsaver actually does not directly touch any GUI at all. The mod works by putting the character in the cutscene controller and dynamically updating the cutscene target with trains as they become active. The base game automatically hides all the player GUI when they're in a cutscene.
To make mod GUIs hidden, I go to the mod portal page and open a bug report for the mod saying that its GUI should be hidden while the player is in a cutscene :) Usually the author agrees, as this is the expected behavior that the base game uses.