When is James really Jacob?

The kid's 5x great grandmother Mary Taylor (nee Thomas) was married in 1877 at the age of 20 and had three children before she died in Georgetown, at the age of 23 and 6 months.  What surprised me was her recorded place of birth, Oakville, which is where I grew up.  Merrick Thomas was a predominant settler of early Oakville, one of roads in Old/downtown Oakville is named after him and the town has preserved Merrick Thomas' house as a museum. Based on Mary Ann's marriage record, I knew that her father was James Thomas and not Merrick but I did wonder if she was somehow related to the famous family. 
  I decided to dig a little and found Mary Ann in the 1861 & 1871 census.  The problem was that the head of the household was Jacob (Nathaniel) Thomas not James.  I searched for and found the baptism record for this Mary Ann Thomas in the Wesleyan Methodist Registers, which a wonderful woman (Ida Reed) transcribed (100,000+ records).  I also found her brother Jacob but for both baptisms, the father's name is Jacob not James.  A review of tax rolls for Trafalgar Township in this time period also do not list James Thomas as a land owner. 
 I did some Google searches using the string "is Jacob the same as James" and discovered that the two names are indeed interchangeable.  I just find it odd that it was done in the marriage record.   
I still wanted to be sure that the connection was correct, so I kept researching.  I did a sideways search of siblings and found something helpful.  All of the children in the 1861/1871 census record stated in their marriage record that their father's name was Jacob except for one brother, who married the year after Mary Ann did.  He too referred to their dad as James. 
  At this point I think I can safely assume that I have the same family which is great because in the course of my research I dug up some interesting information:  Mary Ann's place of residence at the time of her marriage was Toronto which lead me down the wrong path for a bit as I searched the 1881 census for any signs of Jacob and family there. In the end I found Mary Ann (Sr)  living in Georgetown as a widow with a number of her children. Interestingly however, I found Jacob living with his daughter Emma and her husband in Waterloo, where he is  also listed as a widow!  While I haven't found Emma in the 1891 census yet nor have I found Jacob's death record, I did find Mary Ann (still listed as a widow) living in Toronto in 1891.