TOTALLY agree! Same here.MY TLDR at this point: avoid the USB ports in the armrest, and always use Apple cables.
So just to update on this, I've been using both port 1 (USB-C and USB-A) with Apple original cables without problem. The ones in the armrest disconnect with any cable, apple or not. And port 1 disconnects with non-apple cables that work in all other cars I've tried.
As for the armrest ports: Jeep is really screwing up here if the software in the car is activating Apple CarPlay when you plug into them....and then eventually failing. Further, the manual as shown above is ambiguous. It says you can play music through that port, and of course when you plug in your phone to that port, the Jeep chooses to activate CarPlay, and then the music doesn't work because the Jeep loses the connection. Pretty messed up. Just avoid it if you have the same problem.