If the system was perfectly linear, yes.I'm confused. If the system is unstable, shouldn't it be unstable no matter what reference voltage I use?
But a real circuit is never totally linear, thus changes in the operating point can have a small effect on the loop dynamics.
So if the loop is close to instability, it can cause the circuit to become unstable as you change the set-point voltage.
You should do a loop stability analysis.
You can simulate this if you substitute a linear gain block in the feedback loop for the PWM modulator.
You just need to calculate the gain value for the modulator, i.e. what is the change in the average output voltage from the M1 PWM transistor output divided by the change in the modulator input voltage (the plus input of the U3 LM339).





