I can trivially connect the payload subnetwork in such a way that it does not impact the final the output. For example, I could gate it behind relus with large negative biases so that the outputs from the payload neurons are always zero.

Besides, if I'm a defender and am suspicious enough to be modifying my network file, I can just set a random subset of the parameters to zero, simulating dropout, or even just add a small amount of noise to the low order bits of every weight. If the defender is aware enough to modify the network, then I don't think the paper's attack is any more robust than my proposed variation.