focus_set(), which is the built in method to make non-speaking characters darker, has just been fixed with patch 1.1.8.
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I fixed the option buttons triggering bug, just download patch 1.1.6 to fix it.
To answer your question, there are many different ways you could mix this engine with other gameplay, but I would advise against having two obj_scenes objects at once. Checking to see if the other gameplay is 'finished' then adjusting a global variable would probably work best.