What do you mean transparent? Do you mean white background color? Would the pdf or eps file come out the same as set(gcf,'Color','None') as set(gcf,'Color',[1 1 1])?
I used to use whitebg(). But it's not really white background anymore since the default color is [.8 .8 .8]. whitebg() just turns it to [.3 .3 .3]. Same is the function colordef(). I