Depending on where the unit will be positioned on the car, inside te cab or outside, or in the engine compartment, you should also consider some conformal coating to prevent moisture ingress ans defects that can arrive because of vibrations. These are actually the most likely ones to kill an ECU in the long run.
This being said, for electronic protection, a p-mos and tvs option is what most ecus actually have on them, together with some emc/noise protection added. As for fuses on the pcb itself...well, sometimes, depending on the designer, they're there, but most times they aren't.
You already have fuses in the main fuse panel so any additional ones on the ecu itself is superfluous.
Also, current monitoring is the main defense against things going crazy in the ECU. Most automotive h bridge chips have this.
Also, I'd focus more on how noise affects the circuit and undervoltage conditions from like cranking the engine, than those pulsed voltage tests.