I agree that DNA is the way to go from here, but I do think it is quite possible the correct father has been found and detailed here. There are such a lot of positive pointers in the various records.
Regarding the mother, I am not convinced that the Mabel Sayles born 1890 in Wimbledon, as identified in reply #14 by Sparrett is right. There doesn’t seem to be any evidence connecting her to Chatham.
In my opinion, for the birth mother, I would be looking at M. E Brooks, (AKA) Mary Elizabeth Harmer, nee Sayles. There are just too many coincidences to ignore her. She was widowed – last child born in 1906. He was separated from wife – last child born in 1907. Both were working in the same line of furniture work. Her maiden name was SAYLES – not so common. Her Christian name initials were M. E. If they were not living together in 1914/ 1915, there certainly were, not long after.
She signed as M E Brooks on both the birth certificate and on Joseph’s death certificate. It might be interesting to see the original birth registration (rather than the registrar copy) to compare M E Brooks signature with Mary Elizabeth Harmer’s signature on other documents. I certainly would do more research into the Harmer family, and her children.
M. E. Sayles was alone when the baby was born. Her “husband” was away at sea with the navy, and had not been home for months. She would go to a friend, or an employer, or a midwife for the birth of the child – someone who was close. In Chatham, 47 New Street is just around the corner from 4 Boundary Rd – only 7 mins walk (ref google maps).
When she registered the child’s birth, she pretended to be married to Joseph. To hide her real identity she just needed to change Mary Elizabeth to Mabel Edith. She used her correct maiden name, as was required by the paper work – probably nobody in Chatham knew her by Sayles anyway.
It is worth noting that Mary Elizabeth Harmer had a daughter called Edith May, born 2 Dec 1899. (more speculation)
According to family rumour she kept the child for about a year. That may have been true, and when Joseph returned home on leave, it was decided that the child would be adopted. They both had other children who must have been receiving financial support from them.