My understanding of the trutrak autotrim is that when the AP is off, the signal from the manual trim switch to the trim motor is direct so a failure of the auto trim will not have an effect on the trim system.  I also talked to Zach at Trutrak and he says that the relays they use and the system design is set to fail to manual trim.  So it seems unlikely that the AP would be involved in a runaway trim scenario and that the safety trim box would indeed protect against that.