As far as I know, all the preferences programs support SAVE and USE parameters on the commandline.
You specify a preset (which you need to create using the preference program's Save As option) and the USE switch together:
Prefs/screenmode Prefs/presets/myscreenmode.prefs USE
One thing, though, having your shell open on the workbench screen will be a nuisance to intuition which won't want to change the mode until the window is closed (or iconified).