This behavior must have changed at some point. My wife left her fob in the Model S once very soon after getting it in 2016. When the handles retracted, they would not present again after pressing them inward. It also just so happened that at that same time, our Xfinity Internet was down (car connected to our WiFi), so she couldn't connect to the car with the phone app - she wasn't in a rush to go anywhere and just left it until the Internet came back up since she didn't want to deal with hunting for the wifi router and unplugging it.
I first learned about fob in car keeps the car unlocked when I had to have my S towed to the service center. The driver contracts with Tesla and is very familiar with the cars. He told me to leave my fob in the car for the service center. When my handles auto retracted to lock position, I asked him how the service center was going to unlock my car. He pressed on the handles and they presented and told me the car doesn't stay locked if there's a fob inside. This was a month ago.
I can't really explain the difference in behavior. Would they really have separate firmware behaviors for something like this?
-edit-
I re-read your post. I see what you're saying. Back in 2016, it was possible to lock a fob in the car.