I don't have the particular support package installed, so its possible I missed it, but it looks like you perform no filtering on your inputs. However, maybe you are filtering on the TI block in hardware, in which case I apologize. You can either implement a PLL that naturally fiters out this noise, or you can just filter the inputs, and take the phase shift into account. I didn't take a close look at what PLL approach you were using as there are so many, but you could probably just put a low pass filter on the inputs and take into account the phase shift you inject from that. This is especially true since you have a fixed line frequency and the noise from a GaN converter should be pretty far away from 400 Hz.
I would recommend including a plant model in your simulation so that you can test new ideas by injecting noise into the simulation and vetting your approach before attempting it in HW. Maybe you have done that, but the shared model shows the controller only.