As the vehicle wears, it can develop lash in the drivetrain, either its various joints and components or the shock absorbing mounts of the components.
So, when you go from a state of no torque, relaxed, on the drivetrain, to a state of torque, twisting with resistance, in a new vehicle, there is no movement in the drivetrain and thus no noise or clunk vibration, but in a vehicle that has developed lash, that allows for a 1/8 turn of a driveshaft before the resistance stops it, that will creats some noise and clunk vibration. Or, the torque might move engine/trans or a front axle housing more than normal and produce the same thing.
You need to check over the whole drivetrain, inspect for lash at all the joints and replace the joints with lash, check all the mounts for the components look for degraded bushings and replace those.
2 ways to look at it;
- It will come from natural wear on the vehicle and older vehicles will develop these clunks as they get older.
- There is something worn out that needs replacement.
There are some common sense compromises to do with this as well, if its a matter of a couple dollar bushing, you can replace yourself, IMO fix it, if its worn splines on Xfer Case and cost thousands of dollars to fix it, I'd live with the clunk.
There is an argument that shock from the clunk will increase wear on the joints and mounts, and it will get progressively worse, but honestly, the drivetrain should be able to handle it, unless its so bad that the clunk really sounds like there is something really wrong with the vehicle.
Yes, Jeeps that more often have sophisticated 4WD systems compared to other vehicles, will have more of these joints and mounts to wear than most vehicles. So the dealer saying its a Jeep thing is part correct, BUT it is NOT a normal thing. Its a gray area of depending on degrees of how bad the clunk is and what is causing it, as too if its acceptable or NOT, which your dealer should NOT simply be dismissing it, he should be checking it and explaining to you the cause.
It could be simply a bad CV driveshaft or a bad front axle bushing, that they can replace quickly, and you could do yourself or a good independent shop can do fairly cheaply, rarely is anything cheap at a dealership. It might be a little bit of wear in all the joints and mounts in the drivetrain, and on a high mileage vehicle, probably normal wear, and thus it can NOT be fixed cheaply or quickly, you just need to live with it as part of a wearing vehicle that will NOT last forever.