Firestik said that ideally you want the antenna at either rear corner with the base at or above the tub lip. In front, you want it above the hood, like on a pedestal that sticks out between the top of the drivers fender and the closed hood.
Even if you can set your SWR, the antenna still smacks into the jack all day long when you are moving along down the trail. That and you can see the top of the TF bracket moving a little. They could probably add a small gusset there to tune things up.
DISCLAIMER: This is going to be a long post, but for those who don't really understand what's going on in a radio transmitting antenna installation, this may provide some guidance.
Jeeps are really a lot less than ideal for efficient antenna radiation. And radiation efficiency is the bigger issue than SWR. You can have flat antenna SWR and still have a crappy radio transmitting station because of things shielding or redirecting the radiated energy (a la Hi-Lift Jack right next to and parallel to the antenna).
Two major issues are shielding (like I mentioned above) and the ground plane. On a car or pickup, the ideal spot for most efficient mobile operation is centered in the roof. This gets the antenna itself above any shielding metal objects (compare this to firestik's recommendations), but it also places it in the center of the ground plane so that the antenna radiates equally in all directions. The ground plane in this setup helps to focus an essentially spherical radiation pattern and concentrate the radiated energy in a more horizontal direction. This has the effect of a stronger radiated signal, as well as a stronger received signal (think of the receiving benefit like a weak power rifle scope compared to the naked eye).
When we put an antenna at the back of a vehicle, we move the antenna to the rear edge of its ground plane. That makes the radiation pattern somewhat directional toward the front of the vehicle because more of the energy is horizontally concentrated in the front than in the rear. If you now move it to a corner instead of centered in the rear, you skew that directivity diagonally in the longest direction of the ground plane. (For that reason I thought it was a little odd that FireStick recommended a corner, but maybe it has to do with interference from the roll cage?) And if you mount it on the bumper, as we often see, now you have the whole body tub shielding much of the radiated energy in the direction of what would otherwise be the highest effective output. This gives the effect of a weaker signal in both transmitting and receiving.
The Hi-lift right next to the antenna, although we might be able to tune the SWR down to acceptable numbers, will still impact the radiation pattern and the effectiveness of the transmitting antenna -- maybe due to some degree of shielding, or maybe because of parasitic radiation (depending on the frequencies in question and the electrical length of the interfering conductor(s)). The same could be said for the upright support on a roof rack, or even another antenna (say, a ham antenna, commercial VHF, ETC.) This may be negligible for trail use, or it may be significant enough to eliminate communications in some instances.
On a Jeep, because of its inherent design difficulties, it's hard enough to get a well-functioning and efficient antenna installation. No need to further hinder that system by poor placement of the antenna relative to conductive accessories. Some compromises are necessary -- we don't want our antennas mounted as high as a roof mount because they'd be constantly catching on things, to say nothing of the fact that our roofs are not conductive, so there is no ground plane benefit to a roof mount on a Jeep -- but there's no need to shoot yourself in the foot by making needless compromises like carelessly mounting an antenna next to and parallel to components that are electrically conductive, and therefore potentially shielding or redirecting the signal.