Can't both insurance and theft be balanced out in accounting terms?

In other words, they have to move more freight... but it's after-tax profit neutral for them whether they have a huge amount of theft or a little.

Definitely.

This reminds me of patio11’s assertion that the optimal amount of fraud in a system is not 0 because the marginal price of reducing fraud to 0 is far higher than the amount lost to the hardest to eliminate fraud.

The key is to make sure that the costs of eliminating theft are internalized. So as long as the train company reimburses everyone fully then I would imagine they will quickly figure out what the correct level of security is.

At the scale these corporations operate, does it even make sense to insure against theft? The overhead must be significant and on other side premiums should pretty much always be more than claimed.

I would expect that insurance carriers get involved because the load passes through so many hands. Each "hand" needs their own insurance so that they won't just walk off with the load.

However, if it gets expensive enough, I would expect that the parent companies will start to self-insure.