I noticed when searching for Waite, that there was a Waite family in Barton on Irwell, not from Monmouthshire, but if Thomas and Emily heard that there was a family with the same name, perhaps they thought the relatives in Monmouthshire would hear about their location, and changed their name to Harris. Children listed as Harris get married as Waite, Except for the ones baptised as Harris. I am beginning to think this couple did a runner from Monmouthshire, and changed their name to avoid being found, either because they had eloped, or because the police wanted Him/them, and once they had been away long enough the Harris name stuck? When they moved from Barton on Irwell they changed his first name again.
wild imagining I suppse, but am getting stuck for ideas. I think he was Samuel F Waite, because he disappears from the census after 1881.