I believe Bartholomew's father to be JOHN for the following reasons:
WILLIAM of Chowan had children as follows
1. William (born c. 1692).He was tax listed in his own name in 1717 but there is no other mention of him in the records, so he may have died young without issue.I really do no know.
2.Thomas (born c. 1694).He received land in Bertie (carved out of Chowan) in 1723 and removed to Onslow about 1742 and by 1754 was living on the PeeDee River in SC.This is why I think he may be the grandfather of Micajah.I have various land records on the movements of Thomas.
3.John (born c. 1696).By 1743 he had removed to Craven County along the Contentnea Creek.He had moved to Duplin by 1752 and when Bart. begins to acquire land in his own name 8 or 9 years later it is in the same general locale.John had been named by his brother Stephen as guardian of Stephen's minor son William.William later shows up in the Duplin records in close proximity to his uncle John.Bart's son Edmund who died c. 1791 left a note due from John Gainey to Bart.This would seem to indicate that John had a son by the same name who would have been Bart's brother.There are also various land records involving John Gainey, some of a date in all liklihood after the older John would have passed away.None of the sons of William of Chowan ended up in the Duplin/Sampson area except for John.
4.Stephen(born c. 1700) died in 1745 leaving a minor son William and brother John as administrator.When William was an adult he fathered a son Stephen who died serving in the Revolutionary War.
5.Robert (born c. 1705) is mentioned in Court Records in 1732 but there is no other mention of him.I do not know what happened to him.
6.a daughter who married John Hunt in the early 1720's.
I have a 36 page report on all of this prepared for me by a CG, CGL, FASG genealogist, plus I have done much research and pondering for over 25 years.
I would welcome any comments and additional clues which anyone else could provide.Perhaps since William of Chowan had a son named Thomas, the child could have been named for his grandfather, i.e. the Thomas Gaine which you found in Isle of Wight.