I know he means the touch handle. He can't have the key in the ignition because if he has the touch handle then it is push button start and has no ignition. You recommended starting the truck and leaving the key in there when locking the door. With passive entry, you can't do that. If you lock the door and then close it with the key still inside it will unlock the door automatically to prevent you from locking your keys inside. The trucks with regular fob don't do this.
The passive entry trucks behave completely differently than the ones with the standard fob. With the standard fob, the only antenna is inside the ignition switch and it only authenticates the key when it is in the ignition. With the passive entry, there are multiple antennas present and they can tell if the key is inside or outside and the behavior adjusts accordingly.
I don't know about the door open count part; I've never heard of yhwt. What I do know is that no matter what I do the buttons on the fob I used to setup the starter do not work when the truck has been remote started. That makes perfect sense because the truck thinks that key is still in the ignition. The truck authenticated the key when the engine was started, and the ignition has not been turned off yet, so it thinks the key is in there in the RUN position. When a key is in the ignition and the truck is running, the truck ignores all the button presses from that key. You can test that by starting the truck and trying to press buttons on the key while it is still in the ignition.