Because you have a circuit in place to trim your power regulator, you should not disable the Trim/Margin component (or kill the PWM signal) if the rail is ON, otherwise we will see a change in the power regulator voltage output.
That means it is recommended to only disable the Trim/Margin component when the power regulator is off. Even in this scenario, you might want to enable the PWM signal for a short time before enabling the power regulator, only with the purpose to charge the RC circuit, so you will not see any spike when you power the regulator. Because the RC circuit is in there, you might observe a current leakage going through the capacitor, which might cause an overshoot when you enable the power regulator. By charging the circuit before enabling the power regulator, you avoid this overshoot (if the regulator you are using has negative feedback).
For the 100 mV ripple, can you share the parameters inputted in the component and the part number of the power regulator?