I was an exercise physiology major. My exercise physiology class was classified as HEAL. Same with my advanced exercise physiology class. Some of my other classes in my major were classified as OTHR (like EKG interpretation, Principles of Strength Training and Conditioning, and Prevention and Care of Athletic Injuries). The only classes counted towards BCPM in my major were my anatomy and physiology classes.
I entered my exercise physiology classes in AMCAS as BIOL, but they were manually changed by AMCAS after submission to HEAL. We also heavily go into metabolism, learning about glycolysis, glycogen storage, fat metabolism, muscle metabolism and molecular pathways of fiber type change, etc. especially in the context of exercise.
With regards as to if Exercise Physiology or Exercise Science is considered a science LOR, I find it depends on to whom you are talking. In the real world, some employers consider my major as a science and some do not (I've seen in some guidelines, some employers have an asterisk as to what specifically counts as a science degree and state Exercise Science or other related Kinesiology degrees do not count --- even though I technically have a Bachelors of Science :/ ). With regards to med school LOR, I believe I saw on some specific med school websites that they do not count rec letters from Exercise Physiology professors as a science LOR (again denoted by some asterisk or parenthetical). I do not recall which specific schools these were.
Hope that helps.