I've spent the last 48 hours reserching this and I think I have it figured out. Here is what is currently on WT and matches the work of JA Tompkins in 1942:
Stephen Tompkins Sr. [Tompkins-1002], b. 1741, New Castle, NY, d. Kinderhook 1794.
son of Nathniel Tompkins (1011), b. abt. 1705, d. 1771 in Philips, Dutchess, NY, m. Mary Forshay
son of Nathaniel Tompkins, b. 1678 in Salem, MA, m. Mary (Pasco)
son of John Tompkins, b. 1644, Salem, m. one of the duplicate Rebecca Nights.
JA Tompkins went on to write a massive 14 volume work on the Tompkins families between 1957 and 1961 and died while he was finishing it. It has been published in its raw form and we can see that he has fixed a lot of his earlier conflation errors.
Stephen's line then shows:
Stephen Tompkins, b. 1740, NY, father of Hanna Tompkins who married Abraham DeGroff (this matches his DAR records that shows him in Luddington's regiment)
son of Stephen Tompkins, b. 1705, NY, m. Anne (Stephen's brother Nathniel, who married Mary Forshay is listed on the line above, his son Cornelius also served in Luddington's regiment. I found both of them and a third Tompkins who is probably brother to one of these boys and cousin to the other. Note: Luddington's Regiment is in the Dutchess County Miltia, these families are from Dutchess County so far and not from Salem, MA.)
son of Nathaniel, b. 1678, NY, d. 1732, m. Elizabeth Cornell
son of Nathaniel Tompkins, b. 1633, d. 1684 in Rochester, NY, m. Elizabeth White
son of John Tompkins (of Concord), b. 1610, d. Fairfield, Conn., m. Margaret (listed as Goodman, WT research shows UNK)
son of Ralph Tomkins, b. 1585, d. 1666, Bridgewater, MA? m. Katherine Foster, couple migrated to America in 1636
And so, it looks like this line in its last generations is from NY and was conflated into the other line from MA.
I will go in to Stephen's parents/grandparents and disconnect the incorrect wives and merge them with the duplicates and source them as I go.