If it's like modern cars - you drive it to a garage, then plug in a special USB/OBD2 gadget that just disables all tracking and app control. I imagine on a scooter if might be a special cable you plug in somewhere on the motherboard(Playstation modchips anyone?). Unfortunately the underground market is perfectly adept at producing any kind of security override tools for cars, and I can only imagine that once a scooter company like this gets big enough you will be able to buy a $20 "safety override" dongle off Alibaba.
I have no idea why cars are so vulnerable but it is possible to achieve a pretty high level of protection in electronic components. Have a ROM that verifies the integrity of the Flash memory for example. I just found a patent for that even though it's sort of trivial. Overriding ROM is theoretically possible but can be a very costly operation.
In hacks, it's always about the costs. Make the device cheap enough to make the hack expensive enough to discourage theft.
