I'm not sure how to word it in the readme, but I think this is a workaround worth documenting. If you open each layer/gerber file of the design in gerbv (File>Open layer(s)...) then resave it (File>Save active layer as...) gerbv will write the same geometry but in a format that gerbmerge can understand. I was using this method to handle the round pads created by Upverter's gerber output as noted in this gist. Thanks for continuing to work on this script!