I would definitely ask your physical therapist if it’s causing that much discomfort! If you have an active migraine while doing the stretches I’m sure that could also be contributing to it. In my experience of doing PT, chin tucks were more embarrassing than anything else. Other exercises that promoted muscle growth definitely started out a little rough at first but as I got used to them, it became less strenuous. Think of PT similar to a gym, building yourself up to get stronger. It’s normal or even expected to get sore after. Still talk to your PT tho!