You may have found John in Civil War registration - if 44 he would be born 1819, if 47, he would be born 1816. I do have a John Watterson born 1816 to Joseph Watterson and Mary Woods but who knows. He does name his first son Joseph but then again, the one tree that I found with Elizabeth Jane Ferguson on has her parents as Joseph Ferguson and Mary McIntyre. And first son could be named after her father.
I wonder if we could narrow down John's death by other means. Mary Ferguson nee McIntyre (Elizabeth Jane Watterson's mother) died Dec 24, 1876 in Philadelphia. If she had an obit which mentions John Watterson, we would know if he was alive then.
Another thing I noticed is that when Mollie M. Watterson aka Mary McIntyre Watterson, died in 1900, the funeral was held at the home of her aunt Mrs. G. Kennedy. I found the death in 1916 in Pittsburgh of Mary Ferguson Kennedy with parents Joseph Ferguson and Mary McIntyre. Has to be same aunt. It is very doubtful John Watterson would be alive then but if he was, maybe Mary Kennedy's obit would mention him. Some Wattersons lived to age 100. Mary's death certificate says she was born May 1, 1849. However she was 6 on the 1850 census with her widowed mother Mary Ferguson whereas Eliza was 22 which makes Eliza born 1828 rather than 1832 as usually quoted. Eliza is not on the 1860 census with her mother but neither is she with John, that I can find.
