For me the tucked fenders although they can give almost the same clearance and flat fenders when they are high lined, give the jeep a mild/stock look which some people like to go for. some people like the vehicles to look completely stock but have the function of an off roader, some may call it a sleeper wheeler. Others like myself like the untucked variant of our offroad rigs because it obviously gives more clearance but it also gives it a more extreme look. The vehicle is built for business and also when people go to larger and larger tires along with stretched suspensions the untucked will give the ability to still flex with less or any contact. If you were to try to run 42" tires with an axle stretch on tucked fenders then it would make contact unless you increased your bump a lot which would hinder your articulation and in turn reduce the effectiveness of your rig.
Untucked for me for functionality, badass looks, and the ability to go extreme with modifications.