like you said, you can put a flat plate over where the shifter exits the floor and install an aftermarket shift in its place. I did it years ago on a 69 383 4-speed dart I had when I put an auto in it. didn't look weird or bad. It also gives you a cable exit for the new shifter.
wouldnt the floor pan look goofy with the 4 speed hump and no 4-speed shifter? he has a brand new carpet kit for the 4-speed hump. wonder if i could just put a cover over the shifter hole and bolt my b&m shifter to the hump?