You are correct that Francis's will includes the wording, "The Eight Chilldren of my Brother Thomas Kendall, that were living when he my said brother dyed," to whom he gives 20 shilling each, "and this I do in remembrance of the (illegible) I had for, and from, my said loving Brother Thomas Kendall." Part of the section of the will where this appears is illegible.
Thomas Kendall did indeed have eight living children, all married daughters, when he died in 1681. That was 25 years before Francis made his will in 1706, and only five of Thomas' daughters were then living. The illegible section of the will might refer to this, but otherwise I see no provision that the 20 shillings of a deceased daughter was to be paid to her heirs.
I think the will certainly raises the possibility that Francis and Thomas were brothers, but given the fact that there were only five childen then living, I'm a bit uneasy making that claim based on the will alone. I do think that the "disputed origins" section on Francis' profile (which says "other than their name, and presence in early Middlesex County, there is no evidence supporting a relationship") should be softened.
If the PGM project and Francis' PM disagree and think the evidence is conclusive, then I have no issue with making the connection.