Pretty common occurance with the CanBus controlled PWM headlight circuit. TRS/Morimoto builds a pretty insane control harness to overcome this problem when running HID projector headlights basically doing the same thing you're doing. This is a review off their site for that harness. So you aren't alone.
I personally wouldn't tie anything into the PWM controlled lighting circuits on a Mopar vehicles for the reason you're experiencing. That chatter is being caused by the pulsing of current to determine bulb/circuit conditions for protection and indication of a problem. The TRS harness employs a capacitor, load resistors, and a relay control box to overcome this issue. The LED anti-flicker modules you see for TL, KC, Peterson, and JW are similar in construction.
I don't believe there is a simple solution to what you're experiencing other than to modify an anti-flicker harness or start messing around with resistors/capacitors on the coil circuit for the relay to smooth out those pulses.
Some folks are fine with being screwed over, perhaps finding confrontation to be more stressful than just living with whatever the problem is. These are excellent consumers, manufactured to the finest specifications.
Reformed Jeep addict... Jeepless for now.