Currently there is no command to set background transparency.  We should add a "set backgroundTransparency true|false" command to do this so you can put it in a script.  It will call the setBackgroundOpacity() routine in chimera/printer.py.  Until that is added you could use a little Python script transpbg.py:

from chimera import printer
printer.setBackgroundOpacity(True)

and call it from your movie command script with "open transpbg.py"