Well, much to digest. No, Ellen had no occupation on marriage, not until 1930 in fact. Re James: I liked him as a Master Mariner as he does not appear in the census apart from 1881 when he was in port. If he worked out of Hull then retirement to Scarborough would be logical. I also like the 1891 census giving the ages of Joseph & Eliza as I know that she lived into the forties and died in Lytham during WW2.
The marriage of Joseph Wilkinson & Elizabeth Atkin (father James) ticks too many boxes to be a coincidence. However, the fact that Ellen was married under the name Atkin indicates that she was not the product of Joe & Eliza's marriage, so the suggestion that she was born to a sibling of Eliza does hold water. It may be that after Joseph died that Eliza could not afford keep Ellen so she (or both of them) lived with James in Scarborough and James was passed off as Ellen's father rather than her grandfather. This sibling of Eliza is the one to look for I think.
John.