Like I suggested before, and others too, take a Dremel to your current antenna. If you can cut a hole in the fender for a snorkel, you can take a Dremel to the antenna.
If you think you f****ed up royally, you could just go to any Toyota parts dealer and order the stock one and put it back. I tried a stubby, it sucked.
Way back in time, in a distant galaxy, I took a senior level antenna theory class from one of the gods of antennas, Professor Paul Mayes, at the University of Illinois. This guy, with his grad student, came up with the log-periodic antenna, the one used for TVs from the 1960's to when the gubment had the VHF bands shut down for cell phone use. Without boring you to death, short story is the antenna should be a half a wave-length long, and you can put a piece of metal under it to double its effectiveness. Metal underneath, check. Length, um you aint getting the ideal length for 88-108 MHz. But the longer you make it, the better off you are.
All I did was take a look where the white paint marks are on the antenna, and cut that puppy 1/4" shorter. Yes, you loose the round ball at the end. Yes, that round ball does something, its helps with something called "capacitive loading". But guess what, instead of working at 100 miles from the radio tower, maybe its 90 miles from the tower. You still have the CD player that can also play DVDs loaded up with mp3s, you still have the satellite, you have the smart phone bluetooth link, you still have an analog input some place, you still have the USB that you can load music up on. Its not a big deal. Cut the SOB, life is too short. Nobody is gonna give a shit if you whacked the antenna, they are gonna check the miles, check CARFAX, see if you smoked inside the cabin, how many dents and how much rust. I went to the local Toyota dealer cuz he had a red TRD Pro, guaranteed they didn't even notice it, they were probably more concerned about the bright white LEDs, and how to f**k me over properly. (23k for a 2013 Trail? Suck it. Wasn't even worth trying to negotiate).
That thick area on the stubby antenna is windings, an inductor aka choke, it is trying to increase its effective length. Forget it. If you own a Dremel, its way cheaper. and if you don't, you will want one some day.