William and Mary Beverley are probably James brother and sister in law.
James is living with his first wife Elizabeth and child Hannah in Hauxley in 1861, so I think Thomas is probably the father of all of Margarets children.
Shame about the marriage cert fathers details spoiling a good theory. Maybe some kind person can look up the Warenford Prebyterian baptism to see where William and Jane were living at the time of the baptism.
I wonder what happened to Thomas? He is down as being born Watham Hill in Lancashire in 1851. Waitham Hill is a Farm in Kirby Ireleth Parish. Occupied in 1841 census by Farmer John Dixon and family. Includes an 18 year old Thomas Dixon, so thats probably him.
Baptism on LanOPC site :
3 Jun 1821 St Cuthbert, Kirkby Ireleth, Lancashire, England
Thomas Dixon - son of John Dixon & Eleanor. Abode: Waitham Hill. Occupation: Farmer
Alan.