I was looking at my firewall just the other day and thinking about closing up numerous unused holes.
I decided to just use knock-outs from electrical boxes. A little silicone around the edges or a little JB Weld to hold them in place. My thought was to cover the existing hole, not to fill the hole per se. With silicone use they could easily be taken back off if needed.
I figured when painted over they would look like they were supposed to be there.