Don't have a Yoder. Pretty sure most controllers don't have a separate "cool down" mode. You just shut them off, but you mustn't unplug them. That prevents the auger from feeding fresh fuel but keeps the fan on high (seems to be for ~5 minutes) to keep the heat from working its way into your auger and into your hopper while it burns the remaining pellets in the crucible to ash.
But I don't consider that fool-proof so I either:
1. Time my shut-down so I've emptied my hopper and the final cook is with the last remaining pellets still in the auger. Therefore there is no remaining fuel that can burn when I walk away. Or,
2. Remove my meat to rest, then use channel-locks to remove grates and heat deflectors so I can literally see the fire in the crucible. Using a long steel rod I then move the remaining pellets to the opposite side of the crucible from the auger. If there's a large amount of pellets still red hot, I'll add a couple tablespoons of water to help kill the fire without temp stressing or oxidizing the steel. I'll then turn the controller back on for a couple seconds, then off, which resets the max fan for another 5 minutes. Then I walk away.
If you don't do either, I suppose keeping the lid closed is better than open if you
do get a fire feeding back into the auger and hopper since it slightly cuts back reverse air flow in that case.
It sounds like Yoder is using the temp probe to keep the fan going for as long as it senses ANY heat generating occurring in the crucible. Good on them....that's better than
Masterbuilt. But any control system can fail. Or people make mistakes like unplugging their pellet grill. It's a low-probability event, but losing a house or fence or...can be a high-consequence event. Risk management involves understanding/controlling both multipliers.
Bottom line is our outdoor cookers have fewer and less stringent safety controls (and redundancy) than indoor stoves, furnaces, or water heaters. If we don't manage our risk, insurance companies will do it for us.