Looking at the profile, this was discussed pretty heavily earlier this year by Joe C, one of PGM's most senior researchers. The (or at least "A") difficulty seems to be in showing that William the immigrant was also William of Hertford, or really William of Anywhere. The main "Thrale" genealogy book referenced actually seems to show that William son of Raphe stayed in England and died there in 1656, so was NOT William the immigrant. Worth re-reading those comments in detail, I think.
Also, the suggestion was made back then to disconnect the current father (William) from William the immigrant (Thrall-8) which I think does make sense, barring new information or new analysis. I've updated the profile but not yet removed his father giving other folks a chance to weigh in.