My theory is that the r got put in there simply because muskrat is a more common word than muscat. It is the same reason most of us, I assume, have heard, He's in the hospital with prostrate trouble. Prostrate is a more common word that prostate, so prostrate is what we get.
My theory is that the “r” was added into the word “muskrat” since it is more common than “muscat.” For example, “He's in the hospital with prostrate trouble.” Prostrate is a more common that prostate.