Yours is certainly a special situation so it was not covered in the explainer video or the podcast. There are a couple of exercises that require to to raise your hands above your head. One is an overhead squat but you could do that as a normal back squat or bend your elbows without losing the effect. The other is a single arm overhead press but your could press as high as you can or drop this one exercise.
You will get a great deal from this program even without these exercises.