Good find, but this Margdow (in Reply #1) on the banks of Loch Tay is in the parish of Kenmore, not the parish of Blair Atholl, so it may not necessarily be the right Margdow.
The place name element marg is, I believe, from the term merkland, which is an indication of the size or value of a property, and dow is from Gaelic dubh, meaning black or dark. Could there be more than one Margdow? They key to this would be to find Drumchaoin, but so far it is eluding me.
Drum is Gaelic meaning ridge, but I don't know what the second element derives from.
Before rationalisation in 1890-ish there were dozens of small detached enclaves and exclaves of the parishes of Weem, Dull, Kenmore and Killin all round Loch Tay, but not as far as I can make out any detached bits of Blair Atholl.
The nearest kirk to this Margdow would be in the parish of Killin, and it's about 40 miles from the parish kirk of Blair Atholl. Why would they take a baby all that way, or expect the minister of Blair Atholl to travel all that way in the other direction, for the baptism?
I see that Duncan McIntosh and Janet Fraser were married in Logierait in 1769, and had four more sons, all baptised in Logierait: Angus 1773, Donald 1776, Alexander 1779, and William 1783. Duncan junior fits neatly into the gap. Perhaps their stay in Margdow was very short? Have you viewed these other baptisms to see if they contain any clues?
Edit - I wrote the above before seeing Alan Boyd's response.