Just to add...
John was not alone in jumbling up his parental details on his marriage regs. Half sister Susannah was the same

Susan Duff married a James Holt in 1883. Father's details correct, a George Duff...but mother Elizabeth Wilson.
However, details for her death reg from 1903, where daughter Margaret was the informant, father the George D and mother Bridget Thomson. All well again

Notice that Bridget Thomson is showing as deceased by 1903. I think Hugh Cairns died in Camlachie in 1895.
John and Charlotte's son, Hugh Holt Thomson, I wonder if middle name Holt connects to Susan's family. Holt surname not that common in Scotland.