Short answer: just get the antenna tip over the top of the rig. And really, the main reason you want the tip higher than the roof line is to make it easier to set the SWR's.
In theory, and to over-simplify, the best mobile CB antenna is a 102" whip mounted dead-center directly to a metal roof. However, for all intents and purposes on a trail rig a good quality antenna, properly mounted (which almost all of the Jeep-style mounts are) will work just fine.
Some problems with a tall antenna on lifted trail rig are of course hitting branches, or around town breaking a long row of fluorescent lights in a parking garage or under a fast-food drive-thru like a certain Jack-In-The-Box (ask how I know about those two :-) and many 4X4 groups ban certain, especially longer than 4' and stainless steel, antennas on their organized runs. A tall antenna whipping around on a trail can be downright dangerous even if it is tied down (ever see a tied-down antenna break loose? Imagine that thing hitting a spotter or bystander in the head).
The most popular antenna is the old standby 4' or shorter Firestick and it's clones, sturdy, works good and looks nice on a rig. A nice mount is this one (I use it):
http://www.arizonarockyroad.com
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