The Harleys, father and son, were Earls of Oxford and manuscript collectors. They built a huge collection which was later bought for the nation by the British Museum.
The collection included pedigree books. As works of art, basically - nice coats of arms and all. They weren't interested in genealogical accuracy. Neither was the British Museum.
Most of the pedigree books were the collections of antiquaries and arms painters. Sometimes those people got to make copies of Visitations. Sometimes they combined Visitations. They rarely resisted the temptation to make their own amendments and additions.
Those messed-about copies of Visitations became the major source for the Visitation books published in the 19th century. Sometimes they were compared with official versions at the College of Arms, sometimes they weren't. Sometimes the official versions were in a worse state.
Apparently MS 1011 is a copy of the 1582 Visitation, made by a John Saunders, with many additions and continuations of his own, including copies of about half the 1623 Visitation.
MS 1543 began as a copy of 1582 by Richard Mundy, an arms painter, with his own additions. Then in 1623 he lent it to one of the heralds, who did half the Visitation by updating Mundy's copy.
What seems to have happened with Hicks is that somebody collected a not-wonderful pedigree of the Tortworth family down to 1603 (Thomas and his heiress wife Joan are missing).
Then in 1623 Sir William Hicks of Beverston Castle turns up to register his pedigree, but he knows nothing beyond his grandparents.
But somebody at some point thinks the pedigrees must link up, well they're both Hicks and both Gloucestershire, so they put in a dotted line as a guess.
Which was a very bad guess, because when John Hicks died in 38 H 8, 1546-47, the 4-year-old (3 really) was his heir. So Thomas has to be a 2nd son, born about 1545, which makes him younger than his "grandson" Sir Michael.