Yes the muster rolls will show deserted but didn't necessarily mean they were a bona fide deserter. Sometimes when the status was unknown they would be listed as deserted when they were actually missing as a POW, and in some cases the status wasn't known for certain for the rest of the war, as in my friend's ancestor's case. If it wasn't for witnesses verifying his POW status he would have never received a TN pension.
The compiled service records were obtained from the muster rolls, so the compiled record is just as good as its transcription from the original.