Good info. I was worried about interfering with the AM/FM antenna as well.
I did find the FireStik MK-J4R Hood Channel Jeep Antenna Mount Kit

but I've also seen reviews that suggested this was for the older TJ and YJ models. It seems like the sheet metal is a bit flimsy there on the JKs and something banging on the antenna might dork up something. The Arizona Rocky Road is my backup plan, but I was worried about it sticking up too high. The Diamond mount looked interesting, but my Googling around hasn't found much on this particular model of it though.
I could go with a more flexible antenna than a Firestik. Their FireFly seems like it might do the trick, or go with a Wilson antenna.