Looking at Geroge Stoneham on 1891 found him with daughter Elizabeth and her husband Edwin Harris, and daughter Mary. so a Harris name, then going back found Edwin had a brother James.
There is a very short space between Matthew Henry Waite,reg Chorlton 1889, listed as Henry on 1891 census and Eliza Harris registered Chorlton
Have you found baptisms for the children registered as Waite? Where?

Perhaps following my other train of thought, the Harris name popped into their heads, as it was her married sisters name and birth counties given as place of birth, or enumerator a bit slack, and by the next census they were prepared and gave place names.
Perhaps Samuel Waite had left her before after the birth of Matthew Henry, and James turned up to help? and stayed, and was known as Tom , and the enumerator on 1901 knew him as Tom, and put that name and it stuck?
Why they would say Honiton is still a mystery.
I suppose James Harris born Killgwrrg Mon needs eliminating now!!!!