These two sections seem a bit contradictory and the notes on his wife's profile suggest that something is amiss (e.g., why is Drury an additional name for her if she only married another Bacon; i.e., did something get lost in the translation of Visitations data into the one work that is relied upon heavily?
Subtitle this: "Whose cousin?"
If it be admissible - as it seems to be - that Elizabeth BACON was indeed the kinswoman of Col. Nathaniel BACON, Sr., then it is rather more likely that she, though not much his elder, was his paternal aunt than that she was his daughter and, therefore, it is more likely that she was one of the untraced daughters of Sir James BACON (1567, Friston Hall, County Suffolk, England; christened 12 October 1567, St. Dunstan's, London, England - 17 January 1617/18, Friston Hall, County Suffolk, England, England; interred 11 February 1617/18, St. Giles, London, England) and his cousin, Elizabeth BACON (ABT 1573, Hessett, County Suffolk, England - 1649).
Section B: the very words can be found in the source citation, but does it make sense (or is it just me - maybe the two identifying source citations that I found on the spouse's father - James' father-in-law Francis Bacon on a profile which has no Elizabeth Bacon - that suggest an impossible parental relationship due to a pending update to his death date are a false positive match?)
'''The eldest son, Sir James Bacon, by his wife Elizabeth, daughter of Francis and Anne (Drury) Bacon''', left issue Nathaniel Bacon, his son and heir, who was grandfather through his eldest son Thomas, of Nathaniel Bacon of Virginia, "the Rebel," and through his second son, Rev. James Bacon, Rector of Burgate in Suff., by his wife Martha Honeywood, of the other Nathaniel of Virginia, Councellor and acting Governor.''
I just stepped into this because I was wanting to add Barbara Bacon to the correct set of parents. That is all.