Hi Theo,
The Simulink can only download (for the moment) via UART type protocols. Hence you cannot use JTAG based protocols directly from Simulink - BUT - you may generate and built the application from Simulink and get the elf/mot/srec file associated with the application and downloaded via the J-link using an external debugger such as S32 Design Studio that support the JTAG based protocols.
Hope this helps!
Daniel