Although I admit I haven't ploughed through the document helpfully linked, in my recollection from the past the size of an animal that causes damage to a train or infrastructure is relevant to where blame lies.
A large animal should be prevented from getting on to tracks by fencing, and if it does so and is then hit by a train, then clearly the fence is faulty and Network Rail, being responsible for the fence, are responsible for the resulting costs.
A fence will not stop small animals (they can climb over or crawl through) or birds (except ostriches maybe) from reaching the tracks so if they are hit by a train the train operator has to pick up the costs. Larger animals are more likely to have owners than small ones, too.
As an aside, there have been arguments around the size of the animal in the usual buck-passing way.
I think that this principle may have been incompletely understood or stretched beyond reason to make a point. Not unusual...