I don't see a significant issue with a TVS inside the locomotive. Unless it's wired different than the standard MTH and Lionel wiring, the wiring should be able to trip the transformer breaker before it goes up in smoke. The wire used is at least #22 wire, that has an enclosed ampacity of 5 amps, and so should handle the brief overload without issue. Hopefully, you're not leaving the locomotive on the track and repeatedly resetting the breaker! 
How do you guarantee you will know. I have seen plenty of loco with fused wiring either in the tether or at the engine. Motor overload, and power.
5V boards are a perfect example of a hi current failure that would simulate a TVS short. They can hold anywhere from 4 -9 amps. Well below a trigger for some transformers.
A engine sitting on a powered siding as an example.
Frankly we don't have proof they make a difference one way or the other. Though having the one at the transformer makes sense.
The tech note is really apples to oranges. They are talking about protecting discrete components on a PCB. TIU rev L with the SMD TVS added to protect a specific chip is a prime example.
I have one customer with TVS installed in the engine that lost a Audio amp to a derailment. So he is questioning the benefit.
Folks are picking clamping specs with no specific data behind it. TIU have 33, 39, 51 V TVS depending on model and location. Transformers use 51.
But hey, it is a sellable insurance policy. G
