Your drawing above is kind of a mix of activities, states, and actors, but not of hardware systems or network interconnections.
I'd start by modeling the system, not the threats. Perhaps consider creating a UML Communication Diagram showing each of the devices. Then you can start filling in details how data flows from system to system, and how each is initially intended to be protected in whatever ways might make sense (TLS for traffic going over the internet, that kind of thing.)
After you've described how the system is intended to be built, then redraw your model in the Threat Modeling tool. You can then wrap the car in a trust boundary, the bluetooth smartphone device in a different boundary, etc. Your logical borders and your physical borders should start coming together much better then.
The Threat Modeling tool is intended to help analyze a system for security vulnerabilities, it is not really intended to help you initially create the design for a secure system.