Mine is set up like Ken’s. Only the sidings are switched. Not sure you will need two TIUs. I have 4 loops with about 120’ of track each. Also, a hundred or so feet of siding. All on one TIU fed from two PW ZWs.
As for the watchdog issue. I wouldn’t worry about an engine running away if it misses the watchdog signal. They operate in conventional so you would need to toggle the switch twice for a runaway. It happened to me just once when a youngster was playing with a toggle switch.
What you do need to worry about is smoke units. If an engine starts up in conventional, the smoke unit will be on and it will stay on even if you push the start button on the remote. After it starts in conventional, you need to push the start button to put it in DCS mode, then turn off the smoke using the remote…for all engines that started in conventional.