I agree, William Jr. Thorne-29 should be should be son of William Thorne-121 and wife Susannah. I think I might be responsible for putting him with the other couple that includes Sarah Denton, perhaps following a secondary source that had this misidentification.
However, I am wondering whether https://www.wikitree.com/wiki/Thorne-28 (the current father) should exist at all. I have on my near-ish term to-do list to put William Jr. in the right place and figure out what the deal is with this other William Thorne. Somebody had to be the father of Mary Thorne who married Benjamin Mills as per Dedham records ( https://books.google.com/books?id=LMoMAAAAYAAJ&pg=PA67&lpg=PA67&dq=mary+thorne ). Was there really another William Thorne, or is it one person? The note on his profile, from Savage, says "He was prob. liv. at Lynn, when freem. 2 May 1638, and Lewis mades him rem. to L. I. 1642." That sounds like Thorne-121
As for his wife Winifred -- I wrote the rather confusing bio in https://www.wikitree.com/wiki/Linnington-21 when I was still relatively new to genealogy. I think it is worth revisiting it. I need to reactivate my NYGBS membership... for the time being, though, I hope it explains why the family we're talking about here is Linnington, not Livingston.
At the very least, references to Livingston (as opposed to Linnington) don't belong with the wife of Thorne-29. It looks like the only purpose being served by Winifred Livingston-570 and her father Henry Livingston-1234 is in their capacity as wife and father in law of Thorne-29, so they should probably be merged into Linnington-21 and Linnington-3