Well, looking at the 1911 census, Ellen is unmarried and living with her mother and cousin. It doesn't indicate that she had had any children on the census.
In terms of Amelia, the 1911 census states that she had 9 children, 1 of whom had died. This is accurate and the total would include John.
Mary Jane (Amelia's twin) was not married when John was born - but their mother was also Mary Jane. As they would both have shared the same surname when John was born, I cannot tell now if the godmother is Mary Jane senior or Mary Jane junior. No godfather is listed on the register.
I'm currently doing a bit of research into Ellen to see what became of her. She married in 1914 and gave birth to a son, Charles three months later. Her husband died at sea the very next month. She then appears to have had another son born in 1917 - I'm going to request the birth certificate to see what it says. I'm certain it's her because the 1917 baby died in 1918 and the address is consistent with where her sister Mary Jane was living then. So, clearly Ellen was living with her sister, having been widowed. She never remarried and died in the 1950s. On the 1939 census she is still alone, lodging with others it seems. Her occupation is a sack mender, so not very lucrative money-wise one would assume. If she is John's father, maybe the tough time she had explains why she never came forward to claim him as her own? I.e. she wouldn't have been able to support him?
Gosh, it's a very confusing picture. I'm going to request a few certificates relating to Ellen's life to see if I can flesh things out a bit. I don't imagine it will help me unravel the mystery of John's baptism entry!! It would be a lot easier if I could just accept that the priest entered Ellen instead of Amelia by mistake!!