Research note 01: Thomas was found with John and Mary Ann in the 1861 census, listed as their son aged 10. However they did not marry until 1859. The form is clear, so the simplest interpretation is that Thomas is John's son by a previous marriage. Less simple, but possible, he is the son of Mary Ann, and he has taken John's surname instead of the one he was given at birth. The middle initial of R may well be Rackham. The only way to resolve this will be from John and Mary Ann's marriage certificate..
Research note 02: Possibly the soldier who was with the Royal Artillery Barracks on Woolwich Dockyard in 1871 census. Noted as born in Yarmouth. No Thomas Beales born in Yarmouth at around this time was found in later census. Have not found Thomas' millitary papers anywhere.