Both very smooth runners, I'm jealous! In this case I don't personally think it's the driving wheel flanges on the ties, I feel like the frequency of the clicking is too high for that. @MartyE what loco did you observe with this problem?
Two theories: (1) The plastic comb wheel that serves as the tach surface for speed control is rubbing on the sensor or something inside the boiler shell. (2) What you're hearing is "slop" in the dog-bone shaft that connects the motor flywheel to the worm gear. The dogbone could be toggling fore-and-aft in the cups of the U-joints.
To troubleshoot further you could run it with the shell off and observe. That's the first thing I would do. To quiet the dogbone, you could pack a little Vaseline or some viscous moly grease in those cups to stop the ball ends from slapping around. But to totally rule out the dogbone you would have to remove it altogether. Apply power to hear the motor and flywheel by themselves.
Honestly both locos seem to run great. It's just a noise and I wouldn't be that concerned. I don't know your level of mechanical skill. But I would open it up for observation long before I would take the risk of sending it back to Lionel. And yes, there are risks...!!