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You can  change to window mode with windowed=1 on the acsetup.cfg file, but the one in "~/Library/Application Support/Space Quest ][ Remake v2.0 [beta]", not the one inside the application itself.

OMG!  Thank you for this info!

Awesome, hint!  The Windows version comes with a winsetup.exe program.  Does anyone know if there is a similar Mac app?  If not, I'd consider writing a little app which can be used to help configure the settings for Mac versions of games created with the Adventure Game Studio.