Bravo on the very nice summary and chart! I would agree that "Jr.", "secundo", and "tertio" are used simply to designate different persons of same name in age order in the parish, without any reference to genealogical relationships (I have seen the same in German churchbooks of the same vintage).
One possible modification: I think the Margaret who married in 1627 was not the daughter born in 1614 (way too young), but the widow of the William who died 6 months earlier. This would imply that it was the non-emigrant William (your third column) who died in 1627 and Margaret Newmarche who then (re)married to a William Stevenson. No idea then what happened to the William who had married Alice Acey - but I would presume he was out of the picture (either dead or moved away) by 1619/1620, because otherwise we should be counting 4 rather than just 3 Williams in the early 1620s (that is, the William who married Margaret Haiton should be William quarto).