Well I found the problem with my system. I was using the stock limit switch harness, which is designed, I believe, for stepper systems. The three inputs which correspond to the servo axes were jumpered on the back of the 16-pin plug, creating a NC signal regardless of the state of the servo, which applies its signal through the DB25 cable.
After removing the jumpers, a servo fault now halts the system.
Moral: If you want your servo fault to be sensed by the software, be sure that the jumpers on the back of the input line harness are cut or removed. This was in the documentation, but buried pretty deep and not something that jumps out at you.