I see that the original index on SP doesn't say what the surname of Duncan's mother was, just naming her as Mary.
I also note that two other children were baptised in Killin to Donald McMartin and Margaret née McMartin, Duncan, 13 November 1790; Patrick, 13 June 1794. Is it possible, I wonder, that Duncan baptised in 1790 and Duncan baptised in 1791 are actually two records of the same person, the second listing getting his mother's name wrong? It's not unusual for the name Margt (abbreviation for Margaret) to be confused with Mary.
Incidentally, it is customary in Scottish documents to refer to a married woman by her maiden surname, or as 'xxx yyy or zzz' where xxx is her given name, yyy her maiden name and zzz the surname of her husband. She is never referred to as 'xxx yyy zzz', which is open to confusion because in Scotland yyy would normally be interpreted as a middle name.