I believe the story goes like this... First, there is no evidence or reason to think that Henry Howland of Fenstanton, Huntingdonshire was a son of John Howland of co. Essex and a salter in London. It is a mishmash of different theories with no basis in fact.
The original theory came from a document a descendant brought over in the 1830s. This theory and document, which was widely accepted and unchallenged, said that John Howland citizen of London baptized 10 August 1541 married Emme, daughter Nicholas Revell citizen and grocer of London. And that it was his son John Howland who was the Mayflower passenger (and by extention of your Henry Howland).
This was finally disproved and repudiated in the NEHGR in 1880, when it was shown that the son John had died unmarried in London and so of course he was not the Mayflower passenger.
At this time, researchers were aware of the will of Humphrey Howland which is the key proof that Arthur, Henry, and John Howland of New England were his brothers. In 1937, it was discovered by researching the apprentice records of the Draper company of London, that the father of all these Howlands was Henry Howland of Fenstanton.
Nothing is really known of this Henry. He was named as the father of Simon and Henry Howland in the apprentice records (by extension he is the father then also of Arthur, Humphrey, and John). There is a burial record for he and his wife.
There is nothing then to connect Henry of Fenstanton to the John Howland who married Emma Revell. Someone took the new discovery of the name of the father of the New England immigrants, combined it with the old theory regarding John Howland, and created a father for Henry Howland of Fenstanton, Huntingdonshire as John Howland from co. Essex and salter of London. There is no real evidence or connection.
This is my understanding of the error anyways. There is probably a better explanation in the definitive article on Henry Howland: Robert S. Wakefield & Robert M. Sherman, "Henry Howland of Duxbury, Massachusetts, 1633, His Children and His Grandchildren," in NGS Quarterly, 75(June 1987):105-113.