Review the latest trajectory document (TrajectoriesDoc.docx) and source code of TMA. The repository is:
https://gitlab.tekniker.es/aut/projects/3151-LSST/trajectories/trayectorias

The trajectory generation code does not use Simulink but only Matlab code.

The followings are the details from Alberto:

The trajectory generation itself does not need a plant model, since you can test that the generated trajectory meets the movement specifications with the generated data (position, speed, acceleration and jerk). A plant model of the axis does not change the trajectory generation, it just tells the trajectory generator which is the first point. So, the trajectory generator is independent from the axis, and the same trajectory data (starting point, end point, max speed, acceleration and jerk) will produce the same data for different axis.