It looks like Florence Helena Healy nee Walton died just after giving birth to Norah in 1890. There's a record of a burial in Feb 1890 in Walton.
This could explain why you cant find them with the kids as if they married in 1881 after the census and she died in 1890 there's no record of them living together and it explains why the children are usually with her family.
I couldn't find anything on Thomas except the marriage. I expect he must've travelled with his work so maybe that's why the children were born in different areas.