Bondo would not be the best thing to use on that especially without a plug or something to keep the bondo from just falling in. The correct thing to do would be to either plug it up and then use some rage body filler, or if you have access to a welder you could use that to fill in the hole. Either way you would have to have someone paint the hatch or the trunk depending on which one you have which would have to be professional. I would say that if its not that big of deal just leave it but if you hate it and would spend a couple hundred to make it look clean then do it.