All excellent points
No, no proof Ben was in Scotland other than the potential links of shipbuilding and wife's family. Which makes it tenuous and circumstantial on the fact that both cousins married someone of the same name/age
No, no clear Hamilton DNA links, but also no compelling census or other BMD links to John Hamilton. There is a John Hamilton at the claimed address 4 wilton st in the 1881 census, but very little to show where he goes or where he is from then on. He remains a possibility, parents James Hamilton and Mary McAlister, but again no clear DNA links
No, no DNA links at all to Ben Thomas from Birkenhead on either the Thomas or mother Hannah Foley b1834 family lines. He does feature in one family tree and currently they have not done a DNA test, but this could prove or exclude him as an ancestor.
Ancestry DNA breakups suggest very strongly Scottish DNA, which makes the North and south Wales DNA of Ben's parents Thomas/Foley less likely. It does seem more likely that the father should have Scottish DNA so I'm not ruling out the possibility that we're entirely unrelated to Ben Thomas from Birkenhead.
The Macintyre name comes from Jennie's mother's maiden name (Elizabeth Rose MacIntyre) , giving her son the family names of both of her parents in lieu of his father's name. It is 6 months later when John Hamilton gets named as the father of John MacIntyre Macarthur on the register of corrected entries.
Given the strength of the DNA relationship between us and the descendants of John MacIntyre Macarthur I am convinced both Ben and John had the same father. Whether the father was John Hamilton, or Benjamin Thomas, or someone else is so far proving difficult to narrow down.
Thanks for your observations, you're making me critically assess what I know and what I think I know.
If I ve followed correctly there's no proof that Benjamin was ever in Scotland.
Jennie was already pregnant when she married him .
Have you any more distant contacts that show a DNA link to John HAMILTON do you know his mother's name.?
Conversely do you have any distant links which reveal links to Benjamin THOMAS s maternal side
Were the DNA tests with Ancestry ?
Do the ethnic break ups make it most likely that your grandfather had a Scottish or English father .?
Do you know where the the MacIntyre name came from for Jennie's first baby .
I'd personally investigate the Scottish possibilities . John HAMILTON or another John as being father of both babies .