Solution
The observed behavior is expected.
A Real-Time Watchdog restart performs a soft restart of the controller. During this type of restart, the chassis does not completely remove power from all internal supply rails. As a result, trigger and PFI lines can be pulled high by onboard pull-up circuitry.
A manual controller restart performs a hard reset. During a hard reset, the trigger and PFI lines transition low as the system powers down and reinitializes.