How do you know from the census information he was her father, because I would think the relationship is given as granddaughter to the head of household. If she was born illegitimately then whatever she placed on her marriage certificate about the details of her father, may be true or a complete work of fiction. Illegitimate people on marriage did not admit they were illegitimate unless they had to (if their details were known because they were marrying in their home parish for instance). Usually when an illegitimate person married you get a father's surname the same as their own and then perhaps their real father's name, a name of a male relative or just a common ordinary name such as John.
Unless you have the full details of Elizabeth's birth certificate which shows she was born legitimately, it is common to find illegitimate children of daughters living and brought up by their grandparents while their mother's continue to work away as servants, so you can't know for certain without her birth details.
Regards
Valda
