I came across this thread as I had documented Ellen Stewart on Wikitree as part of my trawl through the parish of Raymoghy in 1901 and 1911.
Rebecca's birth record from 1911:
https://civilrecords.irishgenealogy.ie/churchrecords/images/birth_returns/births_1911/01529/1619860.pdf - registered as Duncan with no father
Similarly John's birth record from 1909:
https://civilrecords.irishgenealogy.ie/churchrecords/images/birth_returns/births_1909/01593/1640050.pdf - registered as Duncan with no father
I cannot locate a birth record for Mary.
I can find no marriage records for John other than the original 1897 marriage. I do not believe divorce was possible in Ireland at that time; given the distance between John and his actual wife I would speculate it would be possible to live as husband and wife without too much issue. It is also possible there was no Isabella and the widow status is a cover.
Hope that helps a little.