So if you exit the car with the FOB in your pocket and close all the doors with the engine is still "running" it will honk twice to remind you the engine is still on? Is this the behavior you are talking about? The Prius used to just make one long annoying beep outside the car.
If you exit the car and close all the doors with the FOB -inside- the car with the engine running I -think- it will unlock one of the doors..driver side?
I had weird thing happen just the other day when I opened the passenger side door to get something in the glovebox and realized i wanted to close the panoramic glass shade so I reached over from passenger side to turn car on to accessory mode, closed the shade, pushed the button twice to turn car off (once for engine start and another for OFF right?) and although the display showed the lifetime mileage nothing was actually powering down - I got out of the car and the gauge cluster was still fully illuminated as if I had just started the car in accessory mode. I had to go in the driver's side and turn the car fully on and then off in order to resume normal behavior.