Using pre-defined setup

I have defined some pre-defined setup, so now when the module loads one is prompted to choose one.
Is there an option to load up the game in an “virgin” state without a pre-load? One can then optionally play without it, or use the “file” menu to load that?

Sure. Create a new pre-defined setup in the Editor, but make sure that “Use pre-defined file?” is NOT ticked. Then name it accordingly, e.g. “Blank game”, “Empty map”, or whatever phrase you think best conveys the meaning.