That’s why your truck is behaving like this. There is a feature on the truck called fobik safe. This prevents you from locking the fob inside the truck, hence the three beeps and automatic unlock when it detects the fob inside the cab after the locked door is shut. On the non-passive entry trucks, this is monitored by using four antennas- one under the center seat and one on the back wall to detect the fob inside the cab, and two in the rear doors to detect the fob outside of the cab.
When you configure the truck for passive entry, the rf hub is now looking for a 5th antenna (behind the license plate) to make a determination on where the fob is. If that antenna is not installed, there will be a missing antenna fault stored, and the fobik safe system will go into a failsafe mode. That means that no matter what, if the driver door is open, and the doors are locked using the inside master lock switch, the doors will automatically unlock when you shut the door.