Recognize this is an old post but want to mention that this may indeed have been the case.
I recently came across a baptismal entry made in Canada in 1849.
In the register the margin lists the number of the baptism and name, while the body has a narrative that lists dates, parents, sponsors, and other information.
In this case the margin shows Bridget O'Brien while the commentary states Margaret O'Brien.
I also recall some instances Bridget and Margaret appeared to refer the same child in different censuses. I originally attributed this to the various accents, dialects, and languages in the area at that time (French, English, Scot and Irish Gaelic).
Note that the above birth was during the time of the Great Potato Famine, when many Irish came to Canada. Since emigrants from the same region of Ireland tended to arrive and settle in the same area, it could well be that only a small region of Ireland interchanged these names.
Also, with reference to earlier speculation in this thread that it could relate to needing a saint's name, both Margaret and Bridget (Brigit) are saints names. Brigit lived in the 1300's and Margaret about 300 years earlier.
and the last name of the Parish Priest was Ryan.