The Combe Raleigh birthplace is exactly consistent with James' entry with John, Alice Mary and sister Annie in the 1891 census, and the birth registration confirms his mother's maiden name as Eveleigh, so I don't think there is any real room for doubt that he was theirs.
"James" for the paternal name on the baptism is likely to be a simple slip-up by the Rector - easy enough mistake when the baby's name is James.
