I'm not really sure if this is the best method or if it would cut down on the size at all, but you could create a custom UI sequence and use properties and conditions. Have a dialog with a couple of checkboxes specifying the desired destinations. When the user checks them, set a property to some value to signify that particular destination was selected. Use one feature with one component. In the component tag have the file tag and a couple of filecopy tags in condition statements checking to see if the corresponding properties were set. This way you're only using one copy of the file to do the work. I'm not sure if adding the extra dialog negate any size decrease, though. This was just the first idea that came to mind.
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