Yeah it is puzzling. I have noticed how the name Lillyston changes throughout the research I've done.
My name is Lillyston and it changes on different certificates and sometimes it changes between Lillyston and lillystone throughout just one person's life.
One thing I'm trying to find is the oldest true spelling of the name so I can find out what the surname is supposed to be.
There were variant spellings of most surnames in 19th century and earlier records.
Some people didn't know how to spell their surnames. Whoever was writing their names on a document, (e.g. clergyman, parish clerk, registrar, clerk, lawyer, neighbour) decided how to spell it if the name's holder didn't know. Another scribe might spell the same person's surname differently on another occasion. I've even seen different spellings on the same document.
Chances of variations might have increased when a person who couldn't spell their surname moved to a new place. Faced with a name uncommon in the area + a non-local accent, a scribe would write what s/he heard.
The longer the surname, the more scope for variety. However there were different spellings for even short, simple names. Lamb was one of the commonest surnames in the parish where my Lamb ancestors lived for hundreds of years until 1800s. Surname was occasionally Lambe and Lam in early church registers.