I now have the full story! My Joseph was definately the father of Eliza's daughter's Susannah and Sarah Jane, and son Joseph James. His signature was on his daughter Susannah's birth certificate and is exactly the same signature as the one on his marriage certificate when he married Rachel, 21 years later.
John Stallard died a few months after Eliza married Peter Cato, so that marriage was bigamous. John's death certificate gives his approximate age as 60 and number of years in Australia as about 50 years, informant was the undertaker and all other personal details are lister Not Known, but enough to strongly believe he was Eliza's husband.
Eliza & Peter Cato's marriage certificate gives very little information, other than Peter was a butcher. Peter married again after Eliza's death, and he again used his formal name Peter at marriage, at all other times he used the name Thomas.
The details on Joseph's brother Samuel's death certificate was given by the hospital porter, so probably based on details taken when Samuel was admitted. This leads me to believe Joseph was probably unaware of his death at the time, as he was living and working as a Cab Driver in the Inglewood area. No wife was listed, so I believe Samuel had abandoned Jane and she never did find him.