Not much within reason that you can do to stop a portable oxy torch, and the train doesn't need to be stopped, they just need to hop on and off at the right times. People hop moving trains all the time. All you're doing is shifting the numbers around in the same equation.

But I think the bigger issue is just that you're talking about retrofitting an aspect of the global transport complex. Why would the entire shipping industry change it's approach to standardized containers just to stop some thieves at a specific American spot? The cost of using special containers for this specific route would be prohibitive I imagine, and hard to manage the logistics of.