I like to have a script step Change Theme [Theme Name], that will change the theme during runtime.
The script step should include an option: Apply as default or select a specific layout. If applied as default, all layouts will have the new theme assigned, until it is overruled by this command for a specific layout.
I created a theme for a solution. The client likes it a lot, but also asks for a special them for people with color blindness or another color vision deficiency. Right now I have to duplicate every layout and apply the second theme for the copied layouts and add some (many) script lines that will switch to the right layout.
How much easier would it be, the user selects the theme and a script changes all layouts accordingly.
Another example where this script step would be useful: If the database is accessed with full rights, the lyouts should look a little bit different (perhaps a colorful header or something obvious). The start script could select the special theme when the user logs in as admin.