Can multiple system atrophy affect the heart muscle?

Unfortunately yes: As MSA progresses, every muscle in the body eventually gets affected by the degeneration of the autonomic nerves & other derangements which cannot be compensated for anymore by the "voluntary" nervous system. I have a patient who is likely going through his last stages & it is a relentless disease process for which he now refuses any & all interventions to help him with breathing or swallowing.