Thomas was the illegitimate son of Harriet Annie, and quite probably the son of Thomas Axtell who married her. He was baptised as Thomas Henry Axtell Knibbs just weeks before his mother married Thomas Axtell, but it is seen in the 1901 census, after his mother married Thomas Axtell, that he is listed as Thomas Axtell. Initially I thought this meant that he had dropped the surname Knibbs once his mother married. However, I then went on to discover that he married using the surname of Knibbs so the Knibbs family name carried on through more generations.

From what I can understand, Tom was a very strict father. He had 4 daughters and 2 sons ranging from fairly new born through to 11 years when his wife died, so maybe he had good reason. Apparently he used to hide his daughters' shoes up inside the chimney so that they couldn't go out dancing when he was at work.
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The Wiltshire Conty Council have reference in the Wiltshire and Swindon Archives of a Thomas Henry Axtell Knibbs as being listed in the GWR Pension Fund, indicating he was a railway worker for GWR (Great Western Railways)

Quite possibly, these people appearing in the 1901 census are Lily's parents, brother and maybe even grandmother. We would need to look at the full census record to confirm it.

William Hewitt 25 Berks Reading Berkshire St Giles Baker At Biscuit Factory
Lily Hewitt 25 Berks Reading Berkshire St Giles
William Hewitt 1 Berks Reading Berkshire St Giles
Lily Hewitt 2 Berks Reading Reading S Giles

Mary Hewitt 83 Berks Swallowfield Berkshire St Giles Living On Own Means

Iris worked at Huntley & Palmers, the biscuit makers in Reading, berkshire, England