eh... who spoke about a GUI tick box ? It could be an undocumented feature, with command line option (e.q. "NewGui=0" set in the shortcut). Ideally, another option could be set to prevent starting emulation twice (e.g. NewGui=1, NewAmiga=0), so one could fiddle with GUI settings while the emulation had started, but be prevented to actually start a new instance of the emulator.
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