About 90% of the switch mode power supplies I have seen, use the jelly bean TL431 voltage reference as an error amplifier for correct output voltage. Look for the resistor divider that is connected to the ref pin of the TL431 to play around with that to make the output voltage different. Another idea you can try is just remove all the components that are associated with the TL431 and interface directly to the optocoupler with a DAC output of your Uc and then use an ADC input of the Uc to read output voltage. If you want bulk charging also, then insert a small resistor as a current sense element interfaced to a differential amplifier that you send the output of into another ADC input of the Uc or you can use a fully integrated hall effect sensor such as the 77X series from Allegro Microsystems that you can interface directly to the Uc if you pick one that has a good mV/amp ratio. I like to use the 80mv/amp version which is the ACS770. Finally, you will need to know the minimum current transfer ratio of the optocoupler, which is usually the jelly bean PC817 optocoupler that is made by Sharp Electronics.
My only issue is, can you program in a "software filter" algorithm that mimics active filters and also mimics an integrator? Because they usually wire up the TL431 as a type 2 compensator that acts as an integrator at low frequencies and low pass filter at high frequencies.