The identity of the William Lee who married Alice Felton is not the issue.
The question is, is the William Lee who died in Richmond County in 1717 the same person as the son of William and Alice? (Eleven lines of Y-DNA say he was another man with the same name.)
Unfortunately, *that* William Lee was not considerate enough to leave a will! What we have are some court rulings that his wife Dorothy provided an affidavit that he died intestate and that she was the administrator of his estate. No children are named, and no parents.
Dorothy's mother was apparently one Elizabeth Taylor of the same parish, who left a will on 11 May 1747 specifying various bequests to her, to her other surviving daughter (Sally Ellate), and to various grandchildren and great-grandchildren. It can be inferred from this that Dorothy and William had three(?) children, named as Tom, William, and (maybe) another Dorothy (who seems to have married another man named Lee, about whom absolutely nothing is said). Nothing, however, can be inferred from this document about the parentage of Dorothy's husband.
Dorothy herself does not seem to have left a will either.
Could I believe that William Lee, son of William Constable Lee and Alice Felton, grew up, married a woman named Dorothy (possibly even another Dorothy Taylor), and had children with similar names to the children of William Lee of Richmond and Dorothy Taylor Lee Croucher? Yes, I could - I've seen, and helped to disentangle, more than one example of that sort of thing.
Could I believe that later attempts to trace the various family lines got them muddled up? OH yes. I've seen that happen too.
Could I believe somebody, at some time, jamming the two Williams together when they should have remained separate? You betcha.
IMHO the Y-DNA test fingers the *other* William Lee - the one who *wasn't* the son of William and Alice. And it fingers him times eleven.